title: RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications.
abstract: BACKGROUND
  Soybean 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Our 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.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Chenlong
authors.initials: C
authors.lastname: Cao
authors.forename: Qibin
authors.initials: Q
authors.lastname: Ma
authors.forename: Qiaoying
authors.initials: Q
authors.lastname: Zeng
authors.forename: Haifeng
authors.initials: H
authors.lastname: Wang
authors.forename: Zhihao
authors.initials: Z
authors.lastname: Cheng
authors.forename: Genfeng
authors.initials: G
authors.lastname: Zhu
authors.forename: Ji
authors.initials: J
authors.lastname: Qi
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China. hnian@scau.edu.cn.
authors.forename: Hai
authors.initials: H
authors.lastname: Nian
authors.forename: Yingxiang
authors.initials: Y
authors.lastname: Wang
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate; D017343:Genes, Plant; D018519:Meristem / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D013025:Glycine max / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors