Author Information

Paul L. Auer
R. W. Doerge

Abstract

The soybean genome has undergone many different evolutionary changes that are observable with modern technologies. Of particular interest to scientists and plant breeders is the fact that the soybean genome exhibits features of genome duplication from millions of years ago. Genes that were copied during the duplication event have since diverged functionally. Identifying functionally divergent duplicate genes may provide insight into the evolution of soybean. To investigate functional divergence, transcripts from seven different tissue samples of pooled soybean messenger RNA were sequenced using the Solexa next-generation sequencer and analyzed for gene expression. We tested differential expression of duplicated genes within tissue by employing an integrated normalization and statistical testing methodology. Blocks of duplicate genes (i.e., gene sets) were tested for unanimity of over-or under-expression. These same genes were also analyzed for differential expression across tissues. We identified thousands of duplicate genes that displayed differential expression patterns within each tissue. In some cases these genes were over-represented in duplicate blocks, suggestive of functional divergence of a large genomic region.

Keywords

next-generation sequencing, RNA-Seq, differential expression, soybean

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Apr 25th, 11:30 AM

FUNCTIONAL DIVERGENCE OF DUPLICATED GENES IN THE SOYBEAN GENOME

The soybean genome has undergone many different evolutionary changes that are observable with modern technologies. Of particular interest to scientists and plant breeders is the fact that the soybean genome exhibits features of genome duplication from millions of years ago. Genes that were copied during the duplication event have since diverged functionally. Identifying functionally divergent duplicate genes may provide insight into the evolution of soybean. To investigate functional divergence, transcripts from seven different tissue samples of pooled soybean messenger RNA were sequenced using the Solexa next-generation sequencer and analyzed for gene expression. We tested differential expression of duplicated genes within tissue by employing an integrated normalization and statistical testing methodology. Blocks of duplicate genes (i.e., gene sets) were tested for unanimity of over-or under-expression. These same genes were also analyzed for differential expression across tissues. We identified thousands of duplicate genes that displayed differential expression patterns within each tissue. In some cases these genes were over-represented in duplicate blocks, suggestive of functional divergence of a large genomic region.