Working group session:
Comparative Genomics and Bioinformatics
Presentation type:
oral
Authors:
Locy, Robert ; Hu, Hongtao; Li, Ruijuan; Pant, Shankar; Singh, Narendra ; Weaver, David; Goertzen, Leslie; Locy, Robert ; Hu, Hongtao; Li, Ruijuan; Pant, Shankar; Singh, Narendra ; Weaver, David; Goertzen, Leslie
Presenter:
Locy, Robert ; Locy, Robert
Correspondent:
Locy, Robert ; Locy, Robert
Abstract:
Using over 40 small RNA libraries obtained by deep sequencing of small RNAs from leaves, roots, flowers, and bolls of Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, we have identified as many mature miRNAs, miRNA precursors, and miRNA*s as we could using available genomic sequences and EST collections as references, and a small RNA pipeline that we developed to identify miRNAs and genes in plants. By species these putative miRNAs were classified into 4 groups consisting of: 1) conserved plant miRNAs (found in miRBase18 database in one or more plants, no mismatches) ; 2) novel plant miRNAs (miRNAs not found in miRBase18, but meeting the criteria for annotation of plant miRNAs, i.e. having a miRNA* sequence found in the small RNA library); 3) candidate novel plant miRNAs (miRNAs not found in miRBase18, and lacking predicted miRNA* sequences in any library, but having read numbers greater than 10 reads per million in 2 or more libraries in a species); and 4) miRNA-like sequences (miRNAs not found in miRBase18, and lacking predicted miRNA* sequences in any library, but having read numbers less than 10 reads per million in all libraries in a species). All miRNAs in group 1, 2, and 3 above in each of the 3 species were collapsed into miRNA families, and family representation between the 3 Gossypium species was compared. Using precursors of these miRNAs, phylogenetic analysis was performed on these data, and all plant miRNA precursos found in miRBase18. Tissue specific expression of the miRNA elements in each family will be summarized, and select sequence comparisons of the miRNA precursors from the diploid relatives and tetraploid cotton will be shown. Those sequences which can be mapped to the sequenced D-genome of cotton will be examined, and “hot spots containing multiple miRNA genes will be identified and discussed.