Update tomato chr. 6

Roeland van Ham

Centre for BioSystems Genomics

The Netherlands

Chromosome 6

► Estimated DNA size (54 MB):

| Short arm

Euchromatin: 4.5 µm = 2.7 MBHeterochromatin: 1.8 µm = 11.4 MB

| Long arm

Heterochromatin: 3.5 µm = 22.1 MBEuchromatin: 29.5 µm = 17.7 MB

► Estimated number of BACs to sequence

| ~215

| special regions of interest

disease resistance loci Mi, Cf2/5, Ol1/3

chr. 6 sequencing: project overview

integration with SOL

draft sequence (6X)

phase 1-2

closed sequence

phase 3

CBSG

EU-SOL

Results chr. 6

1. extension BAC selection

2. sequencing; draft & gap closure; 454 sequencing

3. assembly / annotation

4. FISH

Results chr. 6

1. extension BAC selection

► STC approach previously implemented using AFLP fingerprinting

► set-up of SNaPshot Multiplex System for fingerprinting

Results chr. 6

2. sequencing; draft & gap closure

► BACs phase 1-2 64

seed 48 extension 16 BACs in draft sequencing pipeline 8

► BACs phase 3 5

seed 3 extension 2

| BACs in closure pipeline 6

► ~34% (6.9 Mb out of 20.5 Mb) euchr. part draft sequenced

Results chr. 6

► 454 sequencing pilot of 8 (potato) BACs

► GS 20 system requires at least 1/4th of a run

| purchase of instrument (GS FLX ) early 2007 average read length ~250 nt, >100 Mb of raw data, paired-end read procedure

Results chr. 6

4. FISH

► Total number of BACs FISHed: 42+21+28 = 91

| Short arm euchromatin 16

| Long arm euchromatin 36

| Pericentromere heterochromatin 11

| Clearly deviating from genetic map position 13

| On other chromosome, repeat-rich or not done 28

► 2 novel candidate seed BACs in FISH pipeline

Results chr. 6

4. FISH

► Seed BAC distribution over chr. 6: pooled BAC FISH

Filling the gaps – pooled BAC FISH

► 15 short arm euchromatin BACs

► 11 Pericentromere BACs

► 36 long arm BACs

► Establishing the uncovered regions in the euchromatin and heterochromatin parts

Results chr. 6

Results chr. 6

Results chr. 6

4. FISH

► reasonably even distribution of seed BACs

| no oceans, only 5-6 “seas”

| gaps correspond to those identified based on genetic distances

► FISH of new candidate seed BACs for these gaps

► mapping borders of gaps with multicolor FISH

WUR tomato sequencing

► Yuling Bai

► Song Bin Chang

► Erwin Datema

► Mark Fiers

► Joost de Groot

► Mark van Haaren

► Jan van Haarst

► Marleen Henkens

► Thamara Hesselink

► Taco Jesse

► Hans de Jong

► Rene Klein Lankhorst

► Liudmila Khrustaleva

► Chunting Lang

► Pim Lindhout

► Bas te Lintel

► Sander Peters

► Willem Stiekema

► Marjo van Staveren

► Dóra Szinay

► Xiaomin Tang

► Xiao-Bo Zhong