Genome-wide Analysis Of Evolution And Alternative Splicing Event Of HD-Zip Gene Family In Gossypium Ramondii

HD-Zip gene family contains a highly conserved homeobox for encoding transcription factors,and plays an important regulatory role in the proliferation and differentiation of cells. In this research,a comprehensive evolutionary and expression analysis of the Gossypium HD-Zip gene family wereconducted and78HD-Zip genes were predicted and identified. The detailed gene structure,chromosome distribution, phylogenic evolution and modes of alternative splicing were furtheranalyzed and verified.1. According to the evolutionary relationships, we can divide the HD-Zip super family into foursubfamilies. Each subfamily genes have relatively conserved structural features and motifsdistribution. Each HD-Zip family gene could be detected on the chromosomes of cotton, but thedistribution is not even. Some chromosomes have few genes, some have gene clusters.2. Comparing to rice and Arabidopsis, we obtained that during cotton evolution HD-Zip family genesreplication occurs, leading to gene number doubled in cotton. Meanwhile, the distribution of HD-Zipfamily of four subclasses occurs before the separation of species, and some genes have lost in somespecies during the evolution.3. Comparing different periods of cotton fiber development expression deep sequence data couldfound that a large number of HD-Zip genes may be involved in the process of cotton fiberdevelopment. Majority of HD-Zip gene family genes play a important role in0dpa, means that themajority of HD-Zip gene family plays a major role in the initial stage of the fiber. Minority of HD-Zipgene family genes play a less important role in5dpa,10dpa,15dpa and20dpa.4. According to the subfamily data of types of alternative splicing could found that differentorganizations at different times, different gene splicing occurred, and the modes of alternative splicingwere different. All of these might have direct relationship with gene function.In conclusion, this study provided rich information of the cotton HD-Zip gene family whichlayed the foundation for future efforts to study the molecular mechanism of fiber development.