title: Global analysis of the developmental dynamics of Gossypium hirsutum based on strand-specific transcriptome.
abstract: Cotton is an economically important crop that provides both natural fiber and by-products such as oil and protein. Its global gene expression could provide insight into the biological processes underlying growth and development, which involve suites of genes expressed with temporal and spatial control by regulatory networks. Generally, the goal for cotton breeding is improvement of the fiber; thus, most previous research has focused on identifying genes specific to the fiber. However, seeds may also play an important role in fiber development. In this study, we constructed and systematically analyzed 21 strand-specific RNA-Seq libraries for Gossypium hirsutum, covering different tissues, organs and development stages, from which approximately 970 million reads were generated to provide a global view of gene expression during cotton development. The organ (tissue)-specific gene expression patterns were investigated, providing further insight into the dynamic programming associated with developmental processes and a way to study the coordination of development between fiber cells and ovules. Series of transcription factors and seed-specific genes have been identified as candidate genes that could elucidate key mechanisms and regulatory networks in nutrient accumulation during ovule development and in fiber development. This study reports comprehensive transcriptome dynamics at various stages of cotton development and will serve as a valuable genome-wide transcriptome resource for initial gene discovery and functional characterization of genes in cotton.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Yanqin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Gentu
authors.initials: G
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Shoujun
authors.initials: S
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Dayun
authors.initials: D
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Kuang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Fang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Shuangjiao
authors.initials: S
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
authors.forename: Weihua
authors.initials: W
authors.lastname: Yang
mesh_terms: D015536:Down-Regulation; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D009928:Organ Specificity; D010940:Plant Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors