Update tomato chr. 6 Roeland van Ham Centre for BioSystems Genomics The Netherlands.

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Presentation transcript:

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 MB  Heterochromatin: 1.8 µm = 11.4 MB |Long arm  Heterochromatin: 3.5 µm = 22.1 MB  Euchromatin: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  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 1/4 th 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: = 91 |Short arm euchromatin 16 |Long arm euchromatin36 |Pericentromere heterochromatin 11 |Clearly deviating from genetic map position13 |On other chromosome, repeat-rich or not done28 ►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

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