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Shahid Mansoor 1,2, Hui Guo1 and Andrew H. Paterson1
1Plant Genome Mapping Laboratory, University of Georgia, Athens, USA
2Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
Although Gossypium hirsutum has largely replaced G. arboreum and G. herbaceum in the Old World due to superior fiber, there is still considerable interest in the latter two species as important sources of genes for disease and stress resistance. Short RNAs are molecules of 18-24 nucleotides that regulate developmental processes and are a subject of great interest in recent years. The deep sequencing of short RNAs has revolutionized their cloning and millions of short RNA sequences are available in public databases from various tissues of G. arboreum and G. hirsutum. In the present study, short RNA data from G. hirsutum and G. arboreum were compared in silico. The comparison of miRNAs from G. arboreum with validated miRNAs identified several additional families of conserved miRNAs that were found in G. hirsutum data. Several short RNA species in G. hirsutum were related to G. raimondii and were presumably encoded by the D subgenome of G. hirsutum. Interestingly, we also identified 21-24 short RNA species from G. hirsutum that were derived from Cotton leaf roll dwarf virus and were found in leaves, flower and in pre and post-anthesis tissues. There were major differences in the relative abundance of short RNA species from leaf, flower and developing boll. The rapid turn-over of 24 nucleotide long siRNAs in developing fiber tissues was more obvious in G. hirsutum than G. arboreum. Compared to siRNAs, the levels of most of miRNAs were lower in developing fiber tissues and again were more obvious in G. hirsutum. We will discuss implications of these findings toward understanding the role of short RNAs in fiber development and resistance to biotic and abiotic stresses.