update tomato chr. 6 roeland van ham centre for biosystems genomics the netherlands
TRANSCRIPT
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
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
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