Construction Of Functional Genomics Platform Of Gossypium And Non-coding Transcriptome Data Mining

Cotton (Gossypium spp.) is one of the most important natural fiber and oil crops worldwide, comprising about 50 species. Among them, Gossypium hirsutum (G hirsutum) is one of the major cultivated cotton species, derived from the hybridization between two different diploid cotton, Gossypium raimondii and Gossypium arboreum. The studies of G. raimondii and G. arboreum might contribute to the improvement of stress resistance and cotton production in G. hirsutum. In this study, we first built a platform of functional genomics in G. raimondii. Then, we conducted miRNA-seq and degradome-seq approaches and identified salt stress responsive miRNAs and their targets in G. arboreum roots. Through functional enrichment analysis and mining of miRNA-target double-color regulatory network, we studied the potential roles of miRNAs in salt stress response. Meanwhile, we identified some possible siRNA locus in response to water stress in G. arboreum.G raimondii is the first sequenced cotton species. We initially compared the difference of genome assemblies between JGI and BGI versions. Then, we selected JGI version for further studies. We carried out gene family classifications related to signal transduction, transcriptional regulation, secondary metabolism, molecular transport, etc. With the knowledge from other plant species, such as Arabidopsis, we built a predicted protein-protein interaction network. Through topologic analysis and functional annotation on that network, we found out 91 modules related to stress response, signal transduction, transcriptional regulation and secondary metabolism, etc. What’s more, we integrated some known miRNAs and predicted their targets. Moreover, we carried out cotton gene function annotation, including GO, KEGG, MapMan, conserved protein domain and cis-element around promoter region. We further constructed a platform of functional genomics in G. arboreum (GraP: http://structuralbiology.cau.edu.cn/GraP/) with various retrieval toolkits. In addition, cis-element and gene function enrichment analysis tools were also provided to meet users’analysis requirement.G. arboreum is one of the cotton species with genetic robustness and stress resistance. Root is an indispensable plant organ for perception of environmental stimuli, nutrient absorption and hormone production, etc. miRNAs might play important regulatory roles. We studied miRNAs and their possible targets in G. arboreum roots under salt stress using miRNA-seq and degradome-seq.84 salt stress responsive miRNAs were identified through miRNA-seq differential expression analysis and some of them were validated by real-time qRT-PCR. In the meanwhile, we identified the possible targets of miRNAs using degradome-seq technology. Through functional analysis of miRNA targets, we found that miRNA could promote the transition from vegetable to reproductive phase, which might improve stress avoidance through accelerating cotton life cycle. Furthermore, we built miRNA double-color regulatory network. The functional mining results indicated that miRNA also participated in the regulation of hormone related secondary metabolism and signal transduction pathways as well as the crosstalk between biotic and abiotic stresses.siRNA could direct DNA methylation and participate in the regulation of stress response at the epigenetic level. We used our in-house sRNA-seq and mRNA-seq data to identify the possible siRNA loci in response to water stress in G. arboreum. We screened differentially expressed genes related to water stress relevant siRNAs according to positional relationships among siRNAs, DNA repetitive elements and coding genes. GO analysis showed that while those up-regulated siRNA related genes were involved in stress response, signaling, transcriptional regulation and so on, down-regulated siRNA related genes were related to molecular transport.In summary, we here established a platform of cotton functional genomics, and studied water stress related miRNA, siRNA and their biological functions using "omics" approaches. These discoveries might provide knowledge retrieval resource and theory reference to studies of water stress related molecular mechanism and epigenetic regulation in cotton.