A compilation of soybean ESTs: generation and analysis

Author:

Shoemaker Randy,Keim Paul,Vodkin Lila,Retzel Ernest,Clifton Sandra W,Waterston Robert,Smoller David,Coryell Virginia,Khanna Anupama,Erpelding John,Gai Xiaowu,Brendel Volker,Raph-Schmidt Christina,Shoop E G,Vielweber C J,Schmatz Matt,Pape Deana,Bowers Yvette,Theising Brenda,Martin John,Dante Michael,Wylie Todd,Granger Cheryl

Abstract

Whole-genome sequencing is fundamental to understanding the genetic composition of an organism. Given the size and complexity of the soybean genome, an alternative approach is targeted random-gene sequencing, which provides an immediate and productive method of gene discovery. In this study, more than 120 000 soybean expressed sequence tags (ESTs) generated from more than 50 cDNA libraries were evaluated. These ESTs coalesced into 16 928 contigs and 17 336 singletons. On average, each contig was composed of 6 ESTs and spanned 788 bases. The average sequence length submitted to dbEST was 414 bases. Using only those libraries generating more than 800 ESTs each and only those contigs with 10 or more ESTs each, correlated patterns of gene expression among libraries and genes were discerned. Two-dimensional qualitative representations of contig and library similarities were generated based on expression profiles. Genes with similar expression patterns and, potentially, similar functions were identified. These studies provide a rich source of publicly available gene sequences as well as valuable insight into the structure, function, and evolution of a model crop legume genome.Key words: Glycine max, genome sequencing, functional genomics.

Publisher

Canadian Science Publishing

Subject

Genetics,Molecular Biology,General Medicine,Biotechnology

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