The document summarizes updates to the tomato genome sequence including the release of builds SL2.50 and SL3.0. SL3.0 integrated over 1000 BAC sequences into SL2.50, improving contiguity and reducing gaps. Future work includes integrating sequences from chromosome 0, validating the assembly with optical maps, improving gene annotations, and continuing to refine the genome sequence.
Tomato Genome Build SL3.0 Improves Contiguity and Reduces Gaps
1. Tomato Genome Build
SL2.5 SL3.0
Surya Saha, Jeremy Edwards, Prashant Hosmani, Mirella Flores and
Lukas Mueller
Sol Genomics Network (SGN)
Boyce Thompson Institute, Ithaca, NY
ss2489@cornell.edu @SahaSurya
Slides: http://bit.ly/SOL15bld3
2. Tomato Genome
SGN Workshop, SOL 2015
Whole-genome shotgun and full-length
BAC sequences
• 454 reads (filtered, 22X)
• BAC end Sanger reads (0.18X)
• Fosmid end Sanger reads (0.087X)
• Selected BACs
• Sanger reads (5.2X).
3. Tomato Build SL2.40 SL2.50
SGN Workshop, SOL 2015
Lindsay Shearer
Stephen Stack
4. SL2.50 Availability
JBrowse
• Locus pages
• Gene pages
• FTP site
Also at NCBI
http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.3/
SGN Workshop, SOL 2015