short title: evolution and functional conservation of gasts110 in 3 conserved motifs) at their...

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Short Title: Evolution and functional conservation of GASTs 1

Corresponding author 2 Ananda K. Sarkar 3 National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 4 India, 110067. 5 Telephone: +91-11-26735220. Fax: +91-11-26741146. 6 Email: [email protected] 7 8 Title: 9 GAST proteins evolved through successive conjugation of novel motifs and their sub-10 functionalization 11

Ashutosh Kumar, Alka Singh, Pramod Kumar and Ananda K. Sarkar 12

Affiliation 13

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India. 14

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One-sentence summary 16

Exploration of GAST-like genes across the plant kingdom for their structure and evolution 17 through acquisition of novel motifs and functional conservation revealing possible roles in 18 hormone signaling. 19 20 Author contributions 21

AK performed the bioinformatics work and drafted the manuscript. AS and PK performed the 22 experimental work and helped in drafting of the manuscript. AKS conceptualized, designed and 23 revised the manuscript. 24

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Plant Physiology Preview. Published on April 10, 2019, as DOI:10.1104/pp.19.00305

Copyright 2019 by the American Society of Plant Biologists

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Abstract 26

Gibberellic Acid Stimulated Transcript (GAST)-like genes encode small polypeptides, some of 27

which have been implicated in diverse biological processes regulating plant growth and 28

development. However, the occurrence of GASTs among plants, their protein structures, and the 29

mechanisms by which they evolved remain elusive. Here, using a customized workflow, we 30

report genes encoding GAST proteins, identify novel motifs and evolutionary patterns 31

contributing to sub-functionalization of GAST domains, and explore functional conservation 32

across diverse plants. We show that GAST-like sequences evolved initially in the vascular plant 33

Selaginella moellendorffii, after the divergence from bryophytes, and later emerged in 34

gymnosperms and angiosperms. GASTs in angiosperms are characterized by four conserved 35

novel motifs; however, relatively fewer conserved motifs exist in pteridophytes and 36

gymnosperms. Phylogenetic analysis revealed that the GCR1 motif evolved early in S. 37

moellendorffii GAST, which further acquired sub-functionalization through successive 38

conjugation of other motifs and remained conserved across plants, as supported by their 39

collinearity. Functional characterization of two orthologues from the dicot Arabidopsis thaliana 40

(Ath-GASA10) and the monocot rice (Oryza sativa; Osa-GAST9) suggests hormonal regulation, 41

novel roles in seed germination, and functional conservation among diverse plant groups. 42

Computational modelling predicts that these GAST genes are regulated by several factors, 43

including the phytohormones GA and ABA, through conserved cis-motifs present in their 44

promoters, and that they might act as signaling molecules in a complex feedback loop. Thus, our 45

study identifies GASTs and their encoded proteins, uncovers their structure, novel motifs, and 46

evolutionary pattern among plants, and suggests their functional conservation. 47

48 Keywords: GA-Stimulated Transcript (GAST)-like genes, Motifs, Evolution, ABA, seed 49

germination, Selaginella moellendorffii, Gymnosperms, rice. 50

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52 53 54

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Introduction 56

Gibberellins (GAs) are a class of tetracyclic diterpenoid plant hormones involved in the 57

development of root, trichomes, flowers, fruits, leaves, and seeds, as well as stem elongation and 58

leaf expansion (Griffiths et al., 2006). GA signaling functions as a de-repressible system. It is 59

perceived by GA receptor GA-INSENSITIVE DWARF1 (GID1) and interacts with DELLA 60

repressor protein triggering the degradation of DELLA by the ubiquitin-proteasome pathway 61

resulting in the liberation of downstream genes (Ueguchi-Tanaka et al., 2005). 62

Members of Gibberellic Acid Stimulated Transcript (GAST) gene family are regulated 63

by GA and encode small polypeptides having a C-terminal domain of ~60 amino acids. The first 64

member of this gene family, GAST1, was identified as GA-stimulated gene in tomato (Solanum 65

lycopersicum) (Shi et al., 1992). To date, 13 homologues of GAST have been identified in 66

Arabidopsis (Arabidopsis thaliana) (AtGASAs) and most of them are regulated by 67

phytohormones like GA (Roxrud et al., 2007). Members of GAST gene family were found to be 68

involved in various biological processes including shoot elongation and vegetative to 69

reproductive phase transition (GIP1, GIP2, GIP4, and GIP5 of petunia); cell elongation during 70

fruit ripening in strawberry (FaGASA); wounding and pathogen infection in potato (Snakin-1, 71

Snakin-2, and Snakin-3); cell expansion in Gerbera (GEG); panicle differentiation and crosstalk 72

of GA and brassinosteroids signaling in rice (OsGASR1, OsGASR2, and OsGSR1); lateral root 73

formation in maize (Zea mays; ZmGSL1); determination of flowering time (AtGASA4 and 74

AtGASA5); and abiotic stress resistance (AtGASA14) (Kotilainen et al., 1999; Berrocal-Lobo et 75

al., 2002; Ben-Nissan et al., 2004; de la Fuente et al., 2006; Furukawa et al., 2006; Wang et al., 76

2009; Zhang et al., 2009; Rubinovich and Weiss, 2010; Zimmermann et al., 2010; Sun et al., 77

2013; Nahirñak et al., 2016). Since GAST are GA inducible, they may also be involved in GA 78

signaling and biosynthesis, which remains to be studied. 79

GA biosynthesis pathways were first studied in the fungus Gibberella fujikuroi and 80

subsequently in diverse plant species (Hedden et al., 2001). The biochemical origins of different 81

bioactive GAs are found to be from geranylgeranyl diphosphate (GGPP), a common C20 82

precursor for diterpenoids. Though GGPP has not been studied elaborately, GGPP-derived 83

metabolites (bioactive GAs) and their associated enzymes encoded by respective genes are well 84

characterized (Yamaguchi, 2008). Like seed plants, fungi (e.g., G. fujikuroi and Phaeosphaeria) 85

also produce GA, however, GA biosynthesis and signaling vary distinctly from fungi to 86

angiosperms. In fungi, a single bi-functional terpene cyclase is involved in conversion of GGPP 87

to ent-kaurene (a key step in GA biosynthesis). However, the physiological role of GA in fungi 88

has not been identified (Hedden et al., 2001; Hedden and Sponsel, 2015). Physcomitrella patens 89



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(a model bryophyte and early non-vascular land plant/moss), also encodes a single bi-functional 90

terpene cyclase gene, similar to fungi. In the due course of evolution, GA-GID-DELLA 91

signaling components that arose in bryophytes (Hirano et al., 2007) showed no interaction in P. 92

patens, but interacted in early vascular lycophytes/pteridophytes (like Selaginella moellendorffii 93

and Selaginella kraussiana) (Hirano et al., 2007). Subsequently, the GID-DELLA interaction 94

became responsive to GA stimulus and plants started to respond to DELLA-mediated growth 95

arrest (Yasumura et al., 2007). During the evolution of land plants, GA-mediated signaling was 96

refined and seemed to have evolved in parallel with the GA-DELLA system for regulating 97

growth and development. However, our understanding of the regulatory mechanism acting in or 98

downstream of the GA-GID-DELLA signaling remains largely unexplored and enigmatic. 99

Despite the wide presence of GA-GID-DELLA signaling module and the GGPP-derived GA 100

biosynthesis pathway, very little is known about the evolution of downstream/upstream 101

components of GA signaling and their conservation/divergence across the plant kingdom. 102

In the present study, we identify the origin of GASTs, explore the evolution of their 103

orthologs across the plant kingdom, and hypothesize their putative role in the GA signaling 104

pathway. Besides their evolutionary conservation, we also highlight their functional 105

conservation. Here, we outline a workflow for the identification of GAST-like genes across the 106

plant kingdom (from algae to angiosperms). We found that GAST-like genes evolved in vascular 107

plants after the bryophyte divergence, whereas pteridophytes and very few gymnosperms have 108

unannotated GAST orthologs (GORs). GORs have 11 conserved cysteine residues (distributed 109

in 3 conserved motifs) at their C-terminal along with a leucine-rich N-terminal motif in some of 110

the sequences. Phylogenetic studies predicted that GASTs evolved initially with motif1 and 111

acquired sub-functionalization in successive conjugation with other motifs through the activity 112

of transposable elements in S. moellendorffii. The presence of conserved motifs in GAST 113

domain is responsible for the discrete evolution of GORs, which are highly conserved across the 114

plant species. Differential expression analysis indicated that Ath-GASA10 and Osa-GASR9 play 115

a role in seed germination, and mutational studies validated that Ath-GASA10 and Osa-GASR9 116

are functionally conserved in dicots and monocots. In silico annotation analysis suggests that 117

Ath-GASA10 and Osa-GASR9 act as signal molecule for the regulation of the GA biosynthetic 118

pathway either by GA induction or in a negative feedback loop. 119

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Results and Discussion 122

Although the GA signaling pathway is known and extensively studied in angiosperms, the 123

origin, distribution, and evolution of GA-regulated GASTs remains largely unknown (Zhong et 124

al., 2015). We customized a workflow for the identification of GORs across the plant kingdom. 125

Further, we predicted and characterized novel conserved motifs, uncovered their evolutionary 126

pattern, and demonstrated functional conservation (Fig. 1). 127

The GORs evolved in pteridophytes after the divergence from bryophytes 128

Among four angiosperm species studied, we identified 12 and 13 GASTs in maize and tomato, 129

respectively. Among 11 GASTs identified in rice (Oryza sativa), we found one additional 130

sequence Os10g02625 (Osa-GASR11) and 10 GASTs reported previously (Zimmermann et al., 131

2010) (Supplemental Table S1). Similarly, 15 GORs were identified in Arabidopsis, which 132

includes 13 previously known members (Roxrud et al., 2007) and 2 additional GASTs - Ath-133

GASA13 (AT3G10185) and Ath-GASA15 (AT1G10588) (Supplemental Table S1). In the 134

present study, GASTs from Arabidopsis and rice were used as references. Surprisingly, we did 135

not find any GASTs in two gymnosperm species (Picea abies and Pinus taeda). However, we 136

have identified total 18 GASTs in four other gymnosperms (Pinus pinaster, Pinus tabuliformis, 137

Picea sitchensis, and Picea mariana) (Supplemental Table S2) from the NCBI database. Though 138

some of the gymnosperms have orthologs of GA receptor (GID1, SLY1) and DELLA proteins 139

(Vandenbussche et al., 2007), their complete absence in some gymnosperms might be due to 140

successful adaptive modifications which arose in the survived lineages of gymnosperms after the 141

Eocene epoch, where extreme weather conditions (sharp cooling and drying) caused the 142

diversification and extinction of many lineages of gymnosperms, and frequent parallel or 143

convergent evolution (Wang et al., 2000; Ran et al., 2006; Pittermann et al., 2012; Wang and 144

Ran, 2014). However, we cannot rule out the possibility that the absence of GORs in some 145

gymnosperms might be due to the lack of proper annotation. Interestingly, we had identified 11 146

GORs in S. moellendorffii (query coverage >80% and maximum identity >90%), which have not 147

been characterized and annotated previously (Supplemental Table S2). Further, in species like 148

Chlamydomonas reinhardtii and Ostreococcus tauri (unicellular algae), and Physcomitrella 149

patens (bryophyte) we found that some sequences showing less similarity with references 150

(Supplemental Table S2). 151

An unrooted maximum likelihood (ML) tree was reconstructed using 174 protein 152

sequences retrieved from databases. The branches and sub-branches showed very low bootstrap 153

value (>30), however, similar sequences were grouped hierarchically, (Supplemental Fig. S1). In 154

the tree, GOR sequences were distributed in two clusters – cluster-I having highly similar 155



6

sequences and cluster-II having both high and less similar (to reference GASTs) sequences, 156

divided into two sub-cluster (A and B). Sub-cluster A consisted of sequences with less similarity 157

(to references) and sub-cluster B consisted of highly similar sequences from gymnosperms and 158

angiosperms along with pteridophytic S. moellendorffii (Supplemental Fig. S1). The rest of the 159

less similar sequences, from C. reinhardtii, O. tauri (algae), P. patens (bryophytes), P. abies and 160

P. taeda (gymnosperms) grouped separately in cluster-III with a very low bootstrap value and 161

lacked a GAST domain suggesting their un-relatedness to the reference (Supplemental Table S2, 162

Fig. S1). Further, these 94 less similar sequences were eliminated and the remaining 80 163

sequences were used for analysis. 164

The presence of GAST domains and their clustering pattern in the phylogeny 165

(Supplemental Fig. S1) suggest that GORs first evolved in the vascular land plant S. 166

moellendorffii, a pteridophyte, after the divergence from bryophytes, and simultaneously in the 167



7

gymonsperms and angiosperms. However, pteridophytic S. moellendorffii and S. kraussiana 168

possess functional GID1 and DELLA homologs capable of forming a complex with GA, 169

whereas GID1/DELLA-like proteins are unable to form GA-mediated complexes in P. patens 170

(Yasumura et al., 2007; Yamaguchi, 2008). Unlike vascular plants, non-vascular bryophytes (P. 171

patens) lack GA-mediated growth responses due to the absence of a functional GA-GID1-172

DELLA signaling module (Yasumura et al., 2007), which could be the reason for the absence of 173

GORs in bryophytes and algae or vice-versa. 174

Positional conservation of cysteine residues in identified novel conserved GAST-motifs in 175

GORs 176

The screened 80 GORs, with GAST domains, were used for the identification of 177

conserved motifs. Using the MEME suite (Bailey et al., 2009) and multiple sequence alignment 178

(Thompson et al., 1997), we predicted four conserved motifs in 62 highly similar GORs 179

(excluding gymnosperms) (Fig. 2A-E; Supplemental Table S2). Based on the bits value of 180

conserved amino acids, motifs were named as GAST-Cysteine Rich 1 motif (GCR1; 181

x7Cx3Cx2CCx2CxCVPxGx7), GAST-PCY motif (GPCY; PCYx3K[TN]x2G), GCR2 182

(x5Cx3Cx2RCS), and GAST-Leucine Rich motif (GLR) (Fig. 2B-E). Out of four motifs, three 183

were present consecutively at the C-terminal of GAST sequences (Fig. 2A). The GLR has 184

maximum occurrence at the N-terminal with highly conserved leucine residues (Fig. 2E). 185

Though all four conserved motifs were prevalent among GORs, some of the sequences lacked 186

either one, two or three conserved motifs. The GORs from S. moellendorffii also consists of 187

these conserved motifs (Fig. 2A). Smo-GASS10, 11a, and 11b have all four motifs; Smo-188

GASS2a, 2b, and 1 lacks GLR; Smo-GASS8, 9a, and 9b have only GCR1; Smo-GASS7a and 7b 189

lack GPCY motif (Fig. 2A). 190

Similarly, we have identified 5 conserved motifs in 18 GORs from gymnosperms (P. 191

pinaster, P. tabuliformis, P. sitchensis, and P. mariana) (Fig. 3A-F; Supplemental Table S2). 192

Despite important sequence variation, motifs were very similar as described above and were 193

named as gymnosperm GAST-Cysteine Rich 1 motif (gGCR1; x5Cx3Cx2CCx2CxCVPxGx2G), 194

gymnosperm GAST-PCY (gGPCY; PCYx3KTx2[GN]xPKCP), gymnosperm GAST-Cysteine 195

Rich 2 motif (gGCR2; x4Lx4Cx3Cx2RC[KSA]x2), and gymnosperm GAST-Leucine Rich 196

motif (gGLR) (Fig. 3B-F). The GLR has maximum occurrence at the N-terminal with highly 197

conserved leucine residues (Fig. 3E) similar to previous one (Fig. 2E). The fifth novel GAST-198

MSA motif (gGMSA; MSAx5VLY) was also predicted by MEME in some of the gymnosperm 199

GORs Psi-GASP2a, 2b, 9, 11a and 11b (Fig. 3A and F). The presence of three conserved motifs 200

GCR1, GPCY, and GCR2 (Fig. 2B - D); gGCR1, gGPCY, and gGCR2 (Fig. 3B - D), at C-201



8

terminal have 11 highly positionally conserved cysteine residues (Fig. 2 and 3), though their 202

sequences are not identical. Based on the variable size of GAST domain, some level of 203



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functional variation in GASTs was previously assumed (Roxrud et al., 2007), however our 204

results showing tight conservation of cysteine residues in GAST motifs rather suggest functional 205

conservation of GORs, especially those with complete motifs. 206

Conserved GASTs evolved through sub-functionalization of motifs which originated first 207

in pteridophytes 208

The phylogeny, conserved motifs, and multiple sequence alignment revealed that the 209

GORs originated first in S. moellendorffii. Moreover, our observation indicated that the S. 210

moellendorffii sequences have different combinations of motifs (Fig. 2A). We here show the 211

origin and evolution of GAST domain architecture using a TimeTree of S. moellendorffii 212

GASTs. A TimeTree was reconstructed using the Reltime method (Tamura et al., 2012) inferred 213

from the neighbor-joining method with sequences of S. moellendorffii GAST domains. We 214

observed that GCR1 evolved initially in the sequences of Smo-GASS8, 9a, and 9b, suggesting 215

that GCR1 is the most ancient (Fig. 4). Further, in the relative time frame, Smo-GASS7a and 7b 216

evolved with GCR1, 2 and GLR, followed by the evolution of Smo-GASS10, which had 217

acquired GPCY and was the first to possess four complete motifs (Fig. 4). In the subsequent 218

evolution, Smo-GASS11a and 11b have acquired all four motifs. Unexpectedly, Smo-GASS1 219

lost the GLR and remained with GCR1, 2 and GPCY in course if evolution (Fig. 4). The 220

sequences Smo-GASS2a and 2b evolved later from Smo-GASS1 with the same combination of 221

motifs. The GAST domain (comprised of GCR1, 2 and GPCY) and GLR evolved 222

simultaneously in S. moellendorffii with different combinations (Fig. 4). We found that the 223



10

GAST domain motifs are not identical or recurring sequences, suggesting that they are not the 224

repeats of ancient GCR1. Thus, the evolution and rearrangement of motifs did not arise from a 225

duplication event, as S. moellendorffii is an ancient organism with a small genome and a low 226

rate of evolution (Baniaga et al., 2016) and it did not arise from either whole genome duplication 227

or polyploidy events (Banks et al., 2011). Interestingly, it was also found that the S. 228

moellendorffii genome has transposable elements (TEs) in high proportion (37.5%) (Banks et al., 229

2011). It is plausible that the GASTs evolved initially with GCR1 and later acquired sub-230

functionalization through successive conjugation of other motifs through the activity of TEs in 231

S. moellendorffii. 232

The evolution of GAST domain from ancient GCR1 through sub-functionalization is 233

responsible for discrete evolution of GORs 234

To understand the relatedness among the GORs, we reconstructed one unrooted maximum 235

likelihood (ML) tree using GAST domains sequences of 80 short-listed GORs (Fig. 5). In the 236

ML tree, GASTs diverged from two clusters, one containing sequences of Osa-GASR8, Smo-237

GASS8, 9a and 9b and other cluster containing Smo-GASS7a and 7b along with Psi-GASP1. 238

Interestingly, only rice Osa-GASR8 with a low rate of substitution was clustered with Smo- 239

GASS8, 9a and 9b, and Psi-GASP1, also with a very low rate of substitution, diverged from 240

Smo-GASS7a and 7b (Fig. 5). The rest of the GASTs were diverged and grouped into 3 clades, 241

namely I, II, and III. Clade-I and -III have very diverse sequences with highly variable rates of 242

substitution, in comparison to clade-II (Fig. 5). In clade-I, Osa-GASR9 and Zma-Unch1, with 243

high rates of substitution, grouped discretely and evolved faster. Zma-Peamaclein1, 2, and 3, 244

with very high substitution rates, clustered together and diverged from Osa-GASR2. Psi-245

GASP3a and 3b, with similar sequences, were placed discretely in clade-I. However, Psi-246



11

GASP10a and 10b, with similar sequences and high rates of substitution, clustered together and 247

diverged from Smo-GASS10. Amongst four Arabidopsis sequences of clade-I, Ath-GASA7 248

separated with a higher substitution rate from Ath-GASA8, Ath-GASA10, and Ath-GASA15, 249

which grouped together (Fig. 5). The clustering of GORs in this clade might be due to the 250

similarity of motif sequence to Smo-GASS10, which eventually evolved from Smo-GASS7a 251

and b (Fig. 5). 252



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Clade-II consisted of GORs with less variable rates of substitution and divergence and 253

lacked any S. moellendorffii GORs. Osa-GASR4 and Zma-Unch2, with high substitution rates, 254

diverged hierarchically from Sly-GAST10, Sly-snakin2, Psi-GASP14, and Ath-GASA14 (Fig. 255

5). Ath-GASA2 and Ath-GASA3 evolved faster than other Arabidopsis GASA sequences in 256

clade-II. Psi-GASP2a, 2b, 9, 11a, 11b, and Ptb-GASA2 grouped together and diverged from 257

Ath-GASA9 and Sly-snakin2b_p (Fig. 5). Clustering of only these gymnosperm GORs, having a 258

fifth motif, suggests that the relative similarity between their GAST domain or motifs are 259

responsible for their specific clustering in the ML tree and evolutionary pattern. 260

Clade-III consisted of the rest of the S. moellendorffii sequences and some other GORs 261

(Fig. 5). The Smo-GASS1, 2a, 2b, and Osa-GASR were first to diverged in Clade-III. The 262

subsequent divergence has shown hierarchal separation of cluster of identical sequences Smo-263

GASS11a, 11b, and cluster of Osa-GASR11, Ptb-GASA1 (Fig. 4). These Smo-GORs evolved 264

gradually (Fig. 4). Further, Sly-RSI1p, with a high rate of substitution, grouped together with 265

four gymnosperm GASTs, which were diverged from Ath-GASA5. Ath-GASA4 showed higher 266

rates of substitution in clade-III (Fig. 5). The clustering of GORs in these three clades was due to 267

their similarity with the gradually evolved conserved motifs (Fig. 4). Furthermore, these GORs 268

were discretely distributed in the phylogeny due to the variability in occurrence of motifs and 269

distance between the motifs, which shows their discrete evolutionary pattern. 270

Despite variable coverage of collinearity, most GORs show conservation 271

To understand the evolution of GAST and their retention across plant species, we identified 272

duplicated gene pairs in genomic regions that were syntenic using PGDD (Lee et al., 2013). 273

Further, the syntenic pairs were shown as a network (Fig. 6) from the log scores provided by 274

PGDD (Hammoudi et al., 2016). Most of the identified S. moellendorffii GORs showed variable 275

coverage of collinearity with GORs from other species. We observed that 45% of S. 276

moellendorffii GORs were collinear with 22% of GORs from gymnosperm (Pma-GASA5-like, 277

Ppi-GASA5-like, Ppi-Unch8 and 13) (Fig. 6). All S. moellendorffii GORs, except Smo-278

GASS7b, showed collinearity with 60% of Arabidopsis GORs and 81% of rice GORs. Smo-279

GASS7b showed collinearity only with Osa-GASR1, 10, and 11. Similarly, 38% of GORs from 280

S. lycopersicum and 54% of GORs from Z. mays also showed collinearity with 36% of S. 281

moellendorffii GORs (Fig. 6). All the primitive S. moellendorffii GORs (Smo-GASS8/9a/9b) 282

with GCR1 and gradually evolved Smo-GASS7a with GCR1, 2, and GLR shared collinearity 283

only with Arabidopsis GORs (Fig. 6). The possible reason for maximum number of syntenic 284

pairing of GORs between these two species is that both genomes have striking similarity in the 285

form of genome size, gene density, and occurrence of TEs (Banks et al., 2011). Several GORs 286



13

from rice, maize, tomato, and gymnosperms shared collinearity with Smo-GASS10, having all 4 287

motifs, and they clustered together in clade-I indicating their conservation (Fig. 5). The Smo-288

GASSs (1, 2, 6, 4, and 3), gradually evolved after Smo-GASS10, shared collinearity in various 289

capacity with GORs from other species, and clustered together in clade-III, indicating their 290

evolutionary conservation (Fig. 6). Interestingly, the most recent pteridophytic Smo-GASS2a 291

shared collinearity with the next evolved GORs from gymnosperms (Psi-GASP1), Arabidopsis 292

(dicot) and rice (monocot), indicating their conservation and evolutionary lineage. 293



14

Though Selaginella evolved many million years ago, prior to the angiosperms, the 294

sequences of GORs remain unperturbed. The whole genome duplication (WGD) event resulted 295

into higher ploidy level, which was responsible for the evolution and speciation of vascular 296

plants (Barker et al., 2016). Even though all seed and flowering plants have undergone at least 297

one round of polyploidy (Li et al., 2015), it did not strongly affect the sequences of conserved 298

GORs. The possible reason is that unlike more evolved monocots (rice and maize), in wild 299

Arabidopsis weed, selection was not influenced by domestication. 300

Further, 50% and 22% of identified gymnosperm GASTs showed collinearity with 93% 301

Arabidopsis and 72% rice GORs, respectively, besides S. moellendorffii (Fig. 6). Arabidopsis 302

GORs, except Ath-GASA2, shared maximum number of syntenic pairs with gymnosperm GORs 303

(Fig. 6). Interestingly, gymnosperm GORs did not show any synteny with GORs from S. 304

lycopersicum and Z. mays, which are evolutionarily advanced, partly because of influence of 305

domestication. We also observed slight sequence variation in GAST motifs gGCR1, gGLR and 306

the presence of gGMSA in gymnosperms may cause some level of functional diversification, 307

despite overall strong conservation (Fig. 5). Additionally, few sequenced gymnosperms and 308

poor annotation may affect their collinearity with other species. It is possible that more refined 309

sequencing and annotation of diverse gymnosperms may provide better synteny or collinearity 310

of GORs. 311

Additionally, 72%, 27%, and 9% of rice GORs showed collinearity with all of the 312

Arabidopsis GORs, 84% of S. lycopersicum and 50% of Z. mays GORs (Fig. 6). Similarly, only 313

7% of Arabidopsis GORs did not show collinearity with any of the Z. mays GORs, while Ath-314

GASA5, 12 and 13 (20%) did not show collinearity with any of the S. lycopersicum GORs (Fig. 315

6). Likewise, 50% of Z. mays GORs have shown collinearity with 77% of S. lycopersicum 316

GORs (Fig 6). The maximum number of collinear pairs between rice, Z. mays, and S. 317

lycopersicum have shared the collinearity according to the evolutionary pattern of conserved 318

motifs ensuing their conservation (Fig. 6). And the collinearity network suggests that GCR1, 319

along with GPCY and 3 of GAST domain are highly conserved among the syntenic gene pairs 320

across the plant species used in the current study. 321

Ath-GASA10 and Osa-GASR9 acts as a positive regulator of seed germination 322

Earlier reports have suggested that GASTs were induced by hormonal treatment (Shi et al., 1992; 323

Wang et al., 2009; Sun et al., 2013). We selected a pair of related orthologs, Ath-GASA10 324

(dicot) and Osa-GASR9 (monocot), from clade-I (Fig. 5) to experimentally validate their 325

functional conservation through their response to phytohormones. We observed that GA and 326

ABA induced and reduced the expression level of both Ath-GASA10 and Osa-GASR9 in 327



15

Arabidopsis and rice, respectively (Fig. 7A and B), which indicates their role might be in seed 328

germination (Supplemental Fig. S2) as phytohormones GA and ABA play antagonistic roles 329

during seed germination. Earlier, some members of Arabidopsis GASA (AtGASA4 and 330

AtGASA6) family were also found to be involved in seed germination (Olszewski et al., 2002; 331

Roxrud et al., 2007; Zhong et al., 2015). We also observed the expression of Ath-GASA10 was 332

highly induced by GA treatment, whereas ABA treatment reduced its expression in germinating 333

Arabidopsis seeds (Supplemental Fig. S2). 334

Further, to investigate the potential role in seed germination, we have analysed loss-of-335

function mutant of Ath-GASA10 (named as atgasa10-1) and overexpression line of Ath-GASA10 336

and Osa-GASR9 (named as Ath-GASA10OE and Osa-GASR9OE, respectively) in Arabidopsis 337

(Fig. 8A). In control conditions, the atgasa10-1 mutant (89%) showed slower rate of seed 338

germination than wild type (93%) after 120 hr (Fig. 8B). Ath-GASA10OE seeds (92%) showed 339

slightly faster seed germination rate than wild type (81%) after 48 hr (Fig. 8B). Upon treatment 340

with 1 µM ABA after 48 hr, the difference in rate of seed germination between wild type (75%) 341

and atgasa10-1 (53%) increased further, whereas it showed less severe impact on germination of 342

Ath-GASA10OE seeds (79%) (Fig. 8E). Treatment with GA increased the seed germination rate 343

of Ath-GASA10OE (92% at 48 hr) more than that of wild type (83% at 48 hr), indicating a role 344

of Ath-GASA10 in seed germination in a GA-dependent manner (Fig. 8C). This observation was 345

further strengthened by analysing germination rate of transgenic lines seeds after treatment with 346

PAC, which has a contrasting effect on seed germination rate to that of GA (Zhong et al., 2015) 347

(Fig. 8D). Since GA and ABA treatment inversely altered the expression of Ath-GASA10, we 348

asked if the lower seed germination rate of atgasa10-1 upon ABA treatment could be rescued by 349

GA treatment. We observed that application of GA, along with ABA, was able to reduce the 350



16

difference in seed germination between atgasa10-1 and wild type. Upon ABA treatment, only 351

52% of atgasa10-1 seeds germinated after 48 hr, however, GA+ABA treatment could improve 352

seed germination of atgasa10-1 (65%) (Fig. 8F). Overexpression of Osa-GASR9 showed similar 353

seed germination rate as Ath-GASA10OE upon treatment with ABA, GA, and PAC, which 354

indicates the functional conservation of this protein in monocot and dicot (Fig. 8, Supplemental 355

Table S3). 356

Rice Osa-GASR9 can rescue the seed germination phenotype of Arabidopsis atgasa10-1 357

To genetically confirm the functional conservation of Ath-GASA10 and Osa-GASR9, we 358

transformed pAth-GASA10:Ath-GASA10 and pAth-GASA10:Osa-GASR9 binary constructs into 359

the atgasa10-1 background. Lines showing expression levels near to wild type plants were 360

selected for further analysis (Fig. 8A). Seed germination assay of pAth-GASA10:Ath-GASA10 361

(Ath-GASA10comp) and pAth-GASA10:Osa-GASR9 (Osa-GASR9comp) transgenic lines showed 362

that 65% were able to rescue the low germination efficiency of atgasa10-1. Seed germination of 363

pAth-GASA10:Ath-GASA10 and pAth-GASA10:OsaGASR9 transgenic lines in atgasa10-1 364

background were comparable to wild type plants (Fig. 8). These results indicate that both Ath-365

GAS10 and Osa-GASR9 are involved in GA and ABA signaling pathway-mediated seed 366

germination suggesting their functional conservation, which is also evident from their 367

collinearity (Fig. 6). 368



17

Possible regulation and function of Ath-GASA10 and Osa-GASR9, as a putative signal 369

molecule 370

To understand the functional conservation and regulation of Ath-GASA10 and Osa-371

GASR9, we predicted 3D structures of Ath-GASA10 (Fig. 9A) and Osa-GASR9 (Fig. 9C) and 372

their stereo-chemical quality showed 97.4% and 96,3% residues in allowed region of 373

Ramachandran plots, respectively (Fig. 9B and D), confirming stable structures. Both the 374

proteins having conserved cysteine residues showed 42% sequence (Fig. 9E) and 47% structural 375

similarity, which might be due to the presence of conserved motifs. Some of the members of 376

GAST-like genes in Arabidopsis, tomato, rice, and petunia are regulated by GA (Shi et al., 1992; 377

Aubert et al., 1998; Ben-Nissan et al., 2004; Furukawa et al., 2006; Roxrud et al., 2007). Our 378

analysis showed that Ath-GASA10 and Osa-GASR9 expression is antagonistically regulated by 379

both GA and ABA (Fig. 7A and B), indicating their complex regulation which remains elusive. 380

Therefore, we analysed the EC numbers and GO terms of both Ath-GASA10 and Osa-GASR9 381

and annotated their molecular function in metabolic pathways (Supplemental Table S4) using 382

3D structure modelling which indicate some overlapping functions (Supplemental Table S4). 383

Further, we have identified cis-motifs and their distribution in upstream promoter 384

sequences of Ath-GASA10 and Osa-GASR9, and predicted their regulatory function 385

(Supplemental Table S5, Fig. S3). We observed the presence of at least 5 conserved cis-motifs 386

(Supplemental Fig. S3), which may allow the binding of different factor/regulators having 387

different biological functions, such as ABA response, GA signaling/biosynthesis, lateral root 388

development etc. (Supplemental Table S5, Fig. S3). 389

The best consensus putative function derived for Ath-GASA10 indicates its regulatory role 390

in geranylgeranylation (GO:2000112). The geranylgeranylation process implicates the 391

attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from 392

geranylgeranyl diphosphate to one or two cysteine residue(s) at the C-terminus of specific 393

proteins (GASTs have cysteine rich C-termini). The geranylgeranylated protein acts as a 394

membrane anchor (Jiang et al., 1995), also supported by the predicted enzymatic activity 395

through Sphingomyelin phosphodiesterase (EC3.1.4.12), which is involved in a membrane lipid 396

metabolic process (GO:0006643) (Supplemental Table S4). The geranylgeranyl diphosphate is 397

the precursor of GA, ABA, and brassinosteroid biosynthetic pathway (Supplemental Fig. S4). 398

Subsequently, these findings are also supported by the presence of promoter motif4, which is 399

responsive to ABA (Supplemental Table S5). 400

Similarly, the best consensus putative function assigned for Osa-GASR9 indicates its role 401

in carboxylic acid biosynthetic process (GO:0046394), in relation to gibberellin biosynthetic 402



18

process (GO:0009686), and is well supported by the predicted enzymes EC4.1.1.37 and 403

EC1.13.11.12, indicating its involvement in the formation of plant hormones jasmonic acid and 404

GA (Supplemental Table S4, Fig. S4). The presence of promoter motifs involved in the 405

regulation of LR formation, BZR signalling, seed germination, and GA biosynthesis (promoter 406

motif5) further support these regulation (Supplemental Table S5, Fig. S3). 407

Together, our findings suggest that the functionally-conserved Ath-GASA10 and Osa-408

GASR9 might act as signal molecule for the regulation of the GA biosynthetic pathway either by 409

GA-mediated induction and/or in a negative feedback loop through a complex regulatory 410

network involving hormone signalling (Supplemental Fig. S5). Our results show GA- and ABA- 411

mediated regulation of Ath-GASA10 and Osa-GASR9 expression. These computational analysis 412

results provide a hypothetical framework for regulation and function of Ath-GASTs and Osa-413

GASTs, which opens up new avenues for their further characterization and hormonal regulation, 414

and molecular function in different plant physiology and developmental processes. 415

416

Conclusion 417

In vascular plants, GA signaling is mediated by the functional GA-GID1-DELLA signaling 418

module, which is non-functional in non-vascular bryophytes (Yasumura et al., 2007), possibly 419



19

due to the absence of some unknown signaling component. Poorly studied GA-Stimulated 420

Transcripts (GASTs) may be one such component, which have evolved in pteridophytes and are 421

missing in bryophytes. Our results suggest that GASTs are conserved among vascular plants due 422

to the presence of conserved motifs. Phylogenetic studies indicated that GAST with GCR1 motif 423

initially evolved in S. moellendorffii, where GASTs with four motifs evolved through successive 424

conjugation of other motifs and sub-functionalization. 425

The syntenic pair analysis suggests strong conservation of GASTs across vascular plants, 426

which is acquired through moderate reshuffling of sequences. Two closest orthologues from 427

Arabidopsis (Ath-GASA10) and rice (Osa-GAST9) showed structural similarity and functional 428

conservation between dicot and monocot plants and indicated their novel role in seed 429

germination. We also hypothesize that both Ath-GASA10 and Osa-GASR9 are regulated by 430

phytohormones, through conserved motifs in their promoters, and may act as possible signal 431

molecules in a possible feedback loop in GA- or ABA-mediated regulation. 432

433

Materials and methods 434

Identification of GORs and sequence retrieval 435

The devised flowchart (Fig. 1) was used for the identification of GORs from selected 436

representative species with completely sequenced genome from each phylum except the 437

gymnosperms (Supplemental Table S1). Initially, two species from gymnosperm (P. abies and 438

P. taeda) were taken, later GAST orthologs were searched in all sequenced gymnosperm species 439

(Supplemental Table S1). Firstly, we retrieved all GAST family members from rice and 440

Arabidopsis, and used them as reference for the identification of ortholog sequences in other 441

selected genomes using protein BLAST in GRAMENE 442

(http://ensembl.gramene.org/Tools/Blast?db=core) and NCBI database 443

(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGETYPE=BlastSearch&LINK444

LOC=blasthome). The blast parameters used were: query coverage >80% and maximum identity 445

>90%. Species which did not comply with these criteria, reference GASTs domain were 446

searched through iteration using Position-specific Iterated-BLAST (PHI-BLAST) with altered 447

parameter (query coverage >30%, maximum identity >30% and e-value <2) and partial 448

sequences were discarded. The identification of conserved domains in the GAST sequences 449

were manually curated through multiple sequence analysis and using MEME suite v4.11.2 450

(http://meme-suite.org/) and MAST (http://meme-suite.org/tools/mast) (Bailey et al., 2009). The 451

nomenclature used in the present study to specified GAST family members was “Ath-GASA1” 452

to indicate A. thaliana GASA1, and similar pattern was followed for other species. 453



20

Phylogenetic analysis 454

Phylogenetic analysis was done using MEGA6 (Tamura et al., 2013). Separate trees were 455

reconstructed using full protein sequences and with GAST domains. Maximum likelihood (ML) 456

method was used with GTR Substitution model having discrete Gamma distribution among sites 457

(4 categories) and invariant sites (G + I) as rate among sites. The bootstrap value was estimated 458

from 1000 replicates. The ML tree was inferred through BioNJ as the initial tree using heuristic 459

method (Barik et al., 2014; Barik et al., 2015). The identified novel GAST sequence/s were 460

bestowed to GAST family and annotated according to their closeness or relatedness with 461

reference sequence/s as found in ML tree. The S. moellendorffii GORs were termed “GASS” 462

(GA-stimulated in Seleginella) and gymnosperm GORs were “GASP” (GA-stimulated in 463

Pinaceae family) (Supplemental Table S1). 464

Collinearity calculation among GORs 465

To estimate the GASTs conservation among the genomes, syntenic gene pairs were identified 466

for the calculation of collinearity. These GAST pairs were retrieved from the Plant Genome 467

Duplication Database (PGDD; http://chibba.agtec.uga.edu/duplication/index/blast). The PGDD 468

scores of syntenic gene pairs were present in the form of network through Cytoscape v3.6.0. The 469

‘Organic Layout’ was used for the network representation, and further optimized manually to 470

highlight the relatedness among the GOR syntenic pairs in species specific clusters. 471

3-D structure prediction and identification of conserved motif in promoter 472

3D structure was determined using I-TASSER server (The iterative threading assembly 473

refinement) (Supplemental Table S6) (Zhang, 2008; Roy et al., 2010). The functional annotation 474

was predicted on the basis of predicted Enzyme Commission (EC) numbers with active sites, 475

Gene Ontology (GO) terms and Ligand binding sites (Zhang, 2008; Roy et al., 2010; Yang et al., 476

2015). 3D structures of best predicted model of individual proteins were visualised using 477

Chimera version 1.6.2. Further, predicted consensus GO terms and EC numbers for GAST were 478

used for identification of their high-level functions in the biological system through metabolic 479

pathway database KEGG (http://www.genome.jp/kegg/pathway.html). De novo discovery of 480

promoter motifs were carried out using different tools available on MEME suite (v4.11.2). 481

Predicted promoter motifs were compared by aligning with the different transcription factor 482

(TFs) binding sites in eukaryotes (experimentally defined), available at JASPAR CORE 483

database (http://jaspar.genereg.net/) with the help of TOMTOM (MEME Suite). These identified 484

TFs binding sites were further used to identify their respective orthologous genes in Arabidopsis 485

(http://www.arabidopsis.org/). 486



21

Plant materials and growth conditions 487

The seeds of Arabidopsis thaliana Col-0 (ecotype Columbia-0), and a T-DNA insertion mutant 488

atgasa10-1 (Salk_119972) were procured from ABRC. atgasa10-1 (AT5G59845) contains 489

single exon with T-DNA insertion in promoter region and showed 80% reduction in expression 490

level of Ath-GASA10. Seeds were sterilized, germinated, grown and maintained as describe 491

previously (Singh et al., 2012; Singh et al., 2014). 100 seeds of each line were sterilized and 492

sown on ½ MS supplemented with 1 µM ABA, 1 µM GA, 1 µM PAC. Emergence of radical tip 493

was marked as the first sign of seed germination and monitored from 48 hr of plates transfer to 494

22°C and observed up to 120 hr. For rice study, indica rice cultivar IR64 was used. Seed 495

sterilization and germination assay was performed as describe previously (Singh et al., 2016). 496

The germinated seeds were transferred to hydroponic media for their growth and development 497

(Yoshida S., 1976). Further, we have also generated overexpression lines of Ath-GASA10 and 498

Osa-GASR9 in Arabidopsis and rate of seed germination was analysed in Ath-GASA10-Oe, 499

atgasa10-1 and Osa-GASR9-Oe. 500

RNA isolation and relative expression analysis 501

RNA was isolated using TRI-reagent (Sigma-Aldrich) based method, treated with RNase-free 502

DNase I (Thermo Scientific) and 2 μg RNA was converted into cDNA with M-MLV Reverse 503

Transcriptase (Invitrogen, USA) as described previously (Singh et al., 2017). Each sample was 504

analysed in triplicate by real time (RT)-qPCR using 2X Brilliant II SYBR® Master Mix 505

(Agilent Technologies, USA). PCR reaction was placed in ABI PRISM 7900 HT Fast Real Time 506

PCR System (Applied Biosystems, USA). Actin/GAPDH genes and Actin/Ubiquitin were used 507

as endogenous control in case of rice and Arabidopsis, respectively. For relative quantification 508

of transcript abundance ΔΔCT method was used (Livak and Schmittgen, 2001) (primers were 509

listed in Supplemental Table S7). 510

Construction of transgenic plants 511

Ath-GASA10 promoter was cloned in pCAMBIA1301 vector between PstI and NcoI restriction 512

enzyme sites by replacing CaMV35S promoter. Ath-GASA10 coding region (270 bp) was 513

amplified and cloned in pJET1.2 cloning vector and sub-cloned in pCAMBIA1301 vector 514

between BglII and BstEII restriction enzyme sites under the control of CaMV35S promoter for 515

overexpression and under the control of Ath-GASA10 native promoter for complementation 516

construct. Similarly, coding region (309 bp) of Osa-GASR9 was cloned in pCAMBIA1301 517

vector between BglII and BstEII restriction enzyme sites under the control of CaMV35S 518

promoter for overexpression and under the control of Ath-GASA10 native promoter for 519

complementation construct. These constructs were transformed in Arabidopsis plants using 520



22

floral dip method (Clough and Bent, 1998). T1 plants were selected on hygromycin and resistant 521

plants were used for expression level analysis. Homozygous T3 seeds were used for further 522

experiments. 523

524

Statistical analysis 525

For syntenic pair and collinearity network analysis, log scores were provided by PGDD 526

(Hammoudi et al., 2016) Biological experiments were performed at least in three replicates. 527

Error bars indicate standard error for three independent experiments. Statistical significance for 528

all the experiments was evaluated using One-way ANOVA in Excel (Microsoft) and statistical 529

differences were marked as ***: P<0.001, **: P<0.01, *: P<0.05. 530

531

Accession numbers 532

Accession numbers of the genes used in this study are: Ath-Actin7, AT5G09810; Ath-533

Ubiquitin1, AT3G62250; Osa-Actin1, Os03g50885 and Osa-GAPDH, Os08g03290. Other all 534

genes were listed in the Supplemental Table S1. 535

536

Supplemental data 537

The following supplemental materials are available. 538

Supplemental Figure S1. Phylogenetic analysis of GAST orthologs (GORs) in different 539

species. 540

Supplemental Figure S2. Expression analysis of Ath-GASA10 in germinating seeds. 541

Supplemental Figure S3. Prediction of cis-motifs in the promoter of Ath-GASA10 and Osa-542

GASR9 using MEME-suite v4.11.2. 543

Supplemental Figure S4. Biosynthesis pathways of plant hormones retrieved from KEGG

database.

Supplemental Figure S5. The putative functional pathway of Ath-GASA10/Osa-GASR9 544

postulated through in silico analysis. 545

Supplemental Table S1. List of protein and nucleotide sequences identifies across the plant 546

kingdom for the determination of GORs using reference genome. 547



23

Supplemental Table S2. Identified GORs sequences across the selected species from plant 548

kingdom. 549

Supplemental Table S3. Average germination rates (AGR in %) of wild type and transgenic 550

seeds under hormone treatment and control conditions.. 551

Supplemental Table S4. Predicted consensus GO term and EC number of Osa-GASR9 and 552

Ath-GASA10. 553

Supplemental Table S5. Features of promoter motifs identified from Osa-GASR9 and Ath-554

GASA10. 555

Supplemental Table S6. Best predicted 3D model of Ath-GASA10 and Osa-GASR9 with their

C-Score, TM Score and RMSD value (I-TASSER server) along with predicted

Ramachandran Plot statistics of 3D structure.

Supplemental Table S7. List of primers used in the study. 556

Acknowledgements 557

AK thanks SERB, DST, India for National-Post Doctoral Fellowship (NPDF) and PK thanks 558

CSIR, India for fellowship. We acknowledge central instrumental facility of NIPGR. AS 559

acknowledges DBT, Govt. of India for DBT-Research Associate fellowship 560

(BT/PR3292/AGR/2/811/2011). We thank ABRC, USA for Arabidopsis seeds and my lab 561

members Dr. Shalini Mukherjee, Dr. Swati Verma, Dr. Archita Singh and Mr. Sandeep Yadav 562

for critical review of manuscript. 563

564

565



24

Figures legends 566

Fig. 1. Flowchart for the identification of GORs and functional annotation. The existence of 567 GORs were screened across plant kingdom. The rice and Arabidopsis thaliana genomes were 568 taken as references. 3D structures of GAST proteins (I-TASSER) and promoter motifs (MEME, 569 TOMTOM) were predicted for functional annotation (MEME suite and KEGG pathway). 570

Fig. 2. Distribution of conserved motifs in highly similar GORs. (A). Distribution of 571 predicted motifs in 62 highly similar GAST sequences. Conserved motifs were individually 572 represented in (B-E). GCR1 motif (B), GPCY motif (C), GCR2 motif (D) and GLR motif (E). 573 MEME suite v4.11.2. was used for the prediction of motifs. Identified novel GORs were marked 574 (*). 575

Figure 3. Distribution of conserved motifs in GORs from gymnosperm. (A). Distribution of 576 predicted motifs in 18 GAST sequences from P. pinaster, P. tabuliformis, P. sitchensis, and P. 577 mariana. Conserved motifs were individually represented in (B-F). gGCR1 motif (B), gGPCY 578 motif (C), gGCR2 motif (D), gGLR motif (E), and gGMSA motif (F). MEME suite v4.11.2. was 579 used for the prediction of motifs. 580

Figure 4. TimeTree to predict the evolution of S. moellendorffii GASTs containing 581 conserved motifs in a relative time frame. A TimeTree was reconstructed from S. 582 moellendorffii GASTs orthologs using the Reltime method inferred from NJ in MEGA7. The 583 TimeTree indicated the evolution of GASTs according to the presence of conserved motifs. 584 Smo-GASS9a and 9b taken as outgroup and the distance calculated in relative time of 1. On the 585 right side, GAST sequence with their respective motifs were arranged according to their 586 evolution. The Smo-GASS sequences and length of the motifs do not represent actual scale. 587

Figure 5. Unrooted maximum likelihood phylogenetic tree of GORs using MEGA6. The 588 maximum likelihood tree reconstructed using conserved C-terminal domain of 80 GORs. The 589 bootstrap value was estimated from 1000 replicates. The scale bar represents the amino acid 590 substitution rate. Identified novel GORs were marked (*). 591

Figure 6. Collinearity networks among the GORs to understand conservation using 592 Cytoscape v3.6.0. The collinearity network was drawn between syntenic gene pairs by using 593 scores provided by PGDD. The ‘Organic Layout’ was used for the network representation using 594 Cytoscape v3.6.0 and optimized manually in species specific clusters. Specific colors to 595 represent each species (colored nodes) were used for the collinearity network and the colored 596 edges represent specific syntenic gene pairs across the species used for study. The names of the 597 GORs were shortened to adjust in the nodes. For example, “AtG1”: the first two letters represent 598 species name, next letter represents gene name and the numeric value for the family member of 599 the gene family (Supplemental Table S1). 600

Figure 7. Expression pattern of Ath-GASA10 and Osa-GASR9 upon treatment with 601 phytohormones. Relative expression pattern of Ath-GASA10 and Osa-GASR9 upon treatment 602



25

with 10 µM of ABA, BAP, GA, and IAA for 12 hr. (A) Expression of Ath-GASA10 in 603 Arabidopsis seedling at 5 days after germination (dag) . (B) Expression of Osa-GASR9 in rice 604 seedling at 7 dag. Error bars indicate SE of three independent experiments. One-way ANOVA 605 was performed. Asterisks indicate significant statistical differences, ***P<0.001, **P<0.01, 606 *P<0.05. 607

Figure 8. Ath-GASA10 and Osa-GASR9 are functionally conserved in regulation of seed 608 germination. (A) Relative expression level of Ath-GASA10 in wild type (Col-0), atgasa10-1 609 and in T1 plants of pAth-GASA10:Ath-GASA10 (Ath-GASA10comp); expression of OsaGASR9 in 610 T1 plants of pAth-GASA10:OsaGASR9 (Osa-GASR9comp) analyzed by real time (RT)-qPCR. 611 (B-F) Arabidopsis seed germination assay; seeds of wild type, atgasa10-1, Ath-GASA10comp, 612 Osa-GASR9comp, Ath-GASA10OE, and Osa-GASR9OE were sown on ½ MS media with or 613 without phytohormones. (PAC or GA or ABA alone or in combination of GA and ABA. (B) 614 Average germination rate (AGR in %) in ½ MS medium without hormone treatment. (C) AGR 615 in ½ MS supplemented with 1 µM GA. (D) AGR in ½ MS supplemented with 1 µM PAC. (E) 616 AGR in ½ MS supplemented with 1 µM ABA. (F) AGR in ½ MS supplemented with 1 µM GA 617 + 1 µM ABA. Germination experiment was performed in four replicates and 25 seeds were used 618 in each experiment. Error bars indicate standard errors (SE). 619

Figure 9. Modelled 3D structure of Ath-GASA10 and Osa-GASR9 and its quality check. 620 The protein 3D structure of Ath-GASA10 and Osa-GASR9 was predicted and Stereo-chemical 621 quality were checked using I-TASSER and PROCHECK, respectively. 3D model of (A) Ath-622 GASA10 and (C) Osa-GASR9. Ramachandran plot analysis of (B) Ath-GASA10 and (D) Osa-623 GASR9. 3D structure is visualized through Chimera v1.6.2. The α-helix is represented by 624 magenta and coiled-coil in cyan color. (E) Multiple sequence alignment between Ath-GASA10 625 and Osa-GASR9. 626

627

628

Supplementary Data 629

Figure S1. Phylogenetic analysis of GASTs orthologs in different species. Unrooted ML tree of GASTs family members and similar proteins identified through PHI-BlAST from different species using MEGA6. The ML tree was divided into three clustersI, II and III, whereas cluster-II divided into sub-clusters A and B. Cluster-III contained sequences very less similar to the reference (< 30%). The scale bar represents the amino acid substitution rate.

Figure S2. Expression analysis of Ath-GASA10 in germinating seeds. Relative expression levels of Ath-GASA10 in germinating seeds in response to 10 µM GA, 10 µM ABA and 10 µM PAC. After stratification at 4°C/dark, seeds were incubated in ½ MS medium for 4 h at 22°C under light in growth chamber and were followed by incubation for 12 hr in ½ MS medium without (control) or with GA/ABA/ PAC (treatments). Error bars indicate ±SE of three



26

independent experiments. One-way ANOVA was performed. Asterisks indicate significant statistical differences, ***P<0.001, **P<0.01, *P<0.05.

Figure S3. Prediction of cis-motifs in the promoter of Ath-GASA10 and Osa-GASR9 using 630 MEME-suite v4.11.2. (A) Predicted cis-motifs in the promoters of Ath-GASA10 and Osa-631 GASR9. (B) Distribution of predicted cis-motifs in the promoters. The p-value indicates the 632 measure of degree to which a motif sequence matches the pattern found in the sequence. 633

Figure S4. Biosynthesis pathways of plant hormones retrieved from KEGG database. The Geranyl-PP, Gibberellin and Abscisic Acid have been highlighted with dotted red, deep blue and green circles respectively.

Figure S5. The putative functional pathway of Ath-GASA10/Osa-GASR9 postulated through in silico analysis. The putative function of Ath-GASA10/Osa-GASR9 as a signal molecule was determined from predicted GO terms, EC numbers and promoter motifs through I-TASSER, MEME and TOMTOM tools, respectively. The predicted promoter motif might be regulated by TFs responsive to GA and ABA signaling regulating the expression of GAST, which would further get geranylgeranylated with geranyl moiety received from geranylgeranyl diphosphate, a precursor of GA biosynthetic pathway. Further, the geranylgeranylated protein might be moving toward plasma membrane as a signal molecule.

Table S1. List of protein and nucleotide sequences identifies across the plant kingdom for the determination of GORs using reference genome. Identified novel S. moellendorffii and gymnosperm GORs were marked (*) and (†), respectively.

Table S2. Identified GORs sequences across the selected species from plant kingdom.

Table S3. Average germination rates (AGR in %) of wild type and transgenic seeds under hormone treatment and control conditions After 3 days of stratification at 4°C in dark, seeds of atgasa10-1, Ath-GASA10OE, Osa-GASR9OE, Ath-GASA10comp and Osa-GASR9comp were grown on ½ MS and ½ MS supplemented with 1 µM ABA, 1 µM GA, 1 µM PAC and 1 µM GA +1 µM ABA. Germination experiment was performed in four replicates and 25 seeds were used in each experiment.

Table S4. Predicted consensus GO term and EC number of Osa-GASR9 and Ath-GASA10. Predicted best consensus GO terms (based on CscoreGO) and Enzyme Commission (EC) numbers (based on CscoreEC) for the Osa-GASR9 and Ath-GASA10 from I-TASSER.

Table S5. Features of promoter motifs identified from Osa-GASR9 and Ath-GASA10. Predicted promoter motifs along with their matched transcription factor binding sites (experimentally defined), as available at JASPAR CORE database, were identified with the help of TOMTOM (MEME Suite). Their respective interacting transcription factor genes in Arabidopsis thaliana were also identified. P-value defined as the probability that the match occurred by chance



27

according to the null model, E-value define expected number of false positives in the matches and q-value symbolize for the minimum false discovery rate required to include the match.

Table S6. Best predicted 3D model of Ath-GASA10 and Osa-GASR9 with their C-Score, TM Score and RMSD value (I-TASSER server) along with predicted Ramachandran Plot statistics of 3D structure.

Table S7. List of primers used in the study. 634

635



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https://www.ncbi.nlm.nih.gov/pubmed?term=Aubert D%2C Chevillard M%2C Dorne AM%2C Arlaud G%2C Herzog M %281998%29 Expression patterns of GASA genes in Arabidopsis thaliana%3A the GASA4 gene is up%2Dregulated by gibberellins in meristematic regions%2E Plant Mol Biol&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Banks JA%2C Nishiyama T%2C Hasebe M%2C Bowman JL%2C Gribskov M%2C dePamphilis C%2C Albert VA%2C Aono N%2C Aoyama T%2C Ambrose BA%2C Ashton NW%2C Axtell MJ%2C Barker E%2C Barker MS%2C Bennetzen JL%2C Bonawitz ND%2C Chapple C%2C Cheng C%2C Correa LG%2C Dacre M%2C DeBarry J%2C Dreyer I%2C Elias M%2C Engstrom EM%2C Estelle M%2C Feng L%2C Finet C%2C Floyd SK%2C Frommer WB%2C Fujita T%2C Gramzow L%2C Gutensohn M%2C Harholt J%2C Hattori M%2C Heyl A%2C Hirai T%2C Hiwatashi Y%2C Ishikawa M%2C Iwata M%2C Karol KG%2C Koehler B%2C Kolukisaoglu U%2C Kubo M%2C Kurata T%2C Lalonde S%2C Li K%2C Li Y%2C Litt A%2C Lyons E%2C Manning G%2C Maruyama T%2C Michael TP%2C Mikami K%2C Miyazaki S%2C Morinaga S%2C Murata T%2C Mueller%2DRoeber B%2C Nelson DR%2C Obara M%2C Oguri Y%2C Olmstead RG%2C Onodera N%2C Petersen BL%2C Pils B%2C Prigge M%2C Rensing SA%2C Riano%2DPachon DM%2C Roberts AW%2C Sato Y%2C Scheller HV%2C Schulz B%2C Schulz C%2C Shakirov EV%2C Shibagaki N%2C Shinohara N%2C Shippen DE%2C Sorensen I%2C Sotooka R%2C Sugimoto N%2C Sugita M%2C Sumikawa N%2C Tanurdzic M%2C Theissen G%2C Ulvskov P%2C Wakazuki S%2C Weng JK%2C Willats WW%2C Wipf D%2C Wolf PG%2C Yang L%2C Zimmer AD%2C Zhu Q%2C Mitros T%2C Hellsten U%2C Loque D%2C Otillar R%2C Salamov A%2C Schmutz J%2C Shapiro H%2C Lindquist E%2C Lucas S%2C Rokhsar D%2C Grigoriev IV %282011%29 The Selaginella genome identifies genetic changes associated with the evolution of vascular plants%2E Science&dopt=abstract

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https://scholar.google.com/scholar?as_q=The Gibberellic Acid Stimulated-Like gene family in maize and its role in lateral root development&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zimmermann&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1


short title: evolution and functional conservation of gasts110 in 3 conserved motifs) at their...

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