title: Comparative transcriptomic analysis of developing cotton cotyledons and embryo axis.
abstract: BACKGROUND
  As a by product of higher value cotton fibre, cotton seed has been increasingly recognised to have excellent potential as a source of additional food, feed, biofuel stock and even a renewable platform for the production of many diverse biological molecules for agriculture and industrial enterprises. The large size difference between cotyledon and embryo axis that make up a cotton seed results in the under-representation of embryo axis gene transcript levels in whole seed embryo samples. Therefore, the determination of gene transcript levels in the cotyledons and embryo axes separately should lead to a better understanding of metabolism in these two developmentally diverse tissues.
  
  
  RESULTS
  A comparative study of transcriptome changes between cotton developing cotyledon and embryo axis has been carried out. 17,384 unigenes (20.74% of all the unigenes) were differentially expressed in the two adjacent embryo tissues, and among them, 7,727 unigenes (44.45%) were down-regulated and 9,657 unigenes (55.55%) were up-regulated in cotyledon.
  
  
  CONCLUSIONS
  Our study has provided a comprehensive dataset that documents the dynamics of the transcriptome at the mid-maturity of cotton seed development and in discrete seed tissues, including embryo axis and cotyledon tissues. The results showed that cotton seed is subject to many transcriptome variations in these two tissue types and the differential gene expression between cotton embryo axis and cotyledon uncovered in our study should provide an important starting point for understanding how gene activity is coordinated during seed development to make a seed. Further, the identification of genes involved in rapid metabolite accumulation stage of seed development will extend our understanding of the complex molecular and cellular events in these developmental processes and provide a foundation for future studies on the metabolism, embryo differentiation of cotton and other dicot oilseed crops.
authors: Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australia ; Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
authors: Xiaoming
authors: X
authors: Jiao
authors: Xiaochun
authors: X
authors: Zhao
authors: Xue-Rong
authors: XR
authors: Zhou
authors: Allan G
authors: AG
authors: Green
authors: Yunliu
authors: Y
authors: Fan
authors: Lei
authors: L
authors: Wang
authors: Surinder P
authors: SP
authors: Singh
authors: Qing
authors: Q
authors: Liu
mesh_terms: D001483:Base Sequence; D050260:Carbohydrate Metabolism / Q000235:genetics; D002462:Cell Membrane / Q000378:metabolism; D002849:Chromatography, Gas; D018548:Cotyledon / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development*; D004952:Esters / Q000032:analysis; D005227:Fatty Acids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development*; D006072:Gossypol / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D004952:Esters; D005227:Fatty Acids; D010940:Plant Proteins; D014157:Transcription Factors; D006072:Gossypol
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