Abstract
BackgroundSoybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited.ResultsIn this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development.ConclusionsOur results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.
Highlights
Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is an excellent model for studying evolution of duplicated genes
Ribonucleic acid (RNA)-seq reveals ~ 54,000 transcriptionally active genes in soybean To analyze the soybean (G. max) transcriptome as we had previously done for Arabidopsis and zebrafish [21,28,29], we collected 11 tissues from soybean, including root tip, hypocotyl, cotyledon, callus, shoot apical meristem at 6, 17 and 38 day stage, as well as the axillary meristem, inflorescences before and after the meiotic stage, and open flower, and obtained from 111 to 326 million reads of ~50 bp for each sample, with ~30-50 times more data than previous RNA sequencing (RNA-seq) studies in soybean [5,30]
The genic distribution of reads showed that 75% of mapped reads corresponded to exons, while the remaining reads were distributed among introns (10%), intergenic regions (7%) and the splice junctions (8%)
Summary
Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is an excellent model for studying evolution of duplicated genes. Relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited. The most recent WGD in soybean history occurred at about 13 million years ago (mya) [4], more recent than those in the history of the model plants Arabidopsis and rice. The recently sequenced soybean genome with 950 megabase (Mb) (~85% of the estimated total) of assembled sequences has revealed the presence of many thousands of recent paralogs due to WGD [4], making it an excellent model for study the evolution of duplicate genes. The gene annotation in the soybean genome is still incomplete, and can be further improved by using information from genome-wide information of gene expression, including detection of novel transcribed regions and alternative splicing events
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