Tutorial: exploring structural variation using JBrowse, from the tomato 150+ re-seq project

We recently used JBrowse in the 150 Tomato Genome ReSequencing project, and it worked great!

The aim of the 150 Tomato Genome ReSequencing project (http://www.tomatogenome.net) is to reveal and explore the genetic variation available in tomato. Tomato has been selected as target crop because it is economically one of the most important crop species for the Dutch breeding industry, and is one the most important vegetables globally. However, since the tomato shows only limited genetic diversity in commercial breeding lines, valuable alleles will be available in wild tomato relatives. Since breeding and selection was targeted at only a narrow range of desirable agricultural traits, also old breeding material could be source of interesting alleles that have been lost during domestication.

In order to identify the sequence diversity within tomato, 83 genotypes including 10 old varieties, 43 land races and 30 wild accessions were seqeunced. These wild tomato species represent the full range of expected genetic variation around S. lycopersicum that can still be used as potential breeding material.

Sequences have been mapped against the reference genome of S. lycopersicum cv. Heinz (SL2.40) and SNP and INDEL variation has been determined.

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.

The SNP and INDEL variants have been made available using JBowse (http://www.tomatogenome.net/VariantBrowser/) and an tutorial (http://gmod.org/wiki/JBrowse#Tutorials) on how to explore this data resource by the community has been written.

In addition to variants from the 150+ Tomato Genome ReSequencing project, we will add publicly available variant datasets as well.

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