title: Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae-inoculated cotton roots.
abstract: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19-25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and stress responses in plants. Verticillium wilt is a vascular disease in plants caused by the fungal pathogen Verticillium dahliae. The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticillium-inoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium wilt tolerance ('Hai-7124', Gossypium barbadense L., a Verticillium-tolerant cultivar, and 'Yi-11', Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 215 miRNA families identified in the two cotton species. Of them 14 were novel miRNAs. There were >65 families with different expression between libraries. We also identified two trans-acting siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. Interesting, many siRNAs were found with a perfect match with retrotransposon sequences, suggested that retrotransposons maybe one of sources for the generation of plant endogenous siRNAs. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China.
authors.forename: Zujun
authors.initials: Z
authors.lastname: Yin
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Xiulan
authors.initials: X
authors.lastname: Han
authors.forename: Fafu
authors.initials: F
authors.lastname: Shen
mesh_terms: D001483:Base Sequence; D060467:Disease Resistance / Q000235:genetics* / Q000276:immunology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D018517:Plant Roots / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D034741:RNA, Small Interfering / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D017423:Sequence Analysis, RNA; D054852:Small Molecule Libraries; D020172:Verticillium / Q000502:physiology
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D018626:Retroelements; D054852:Small Molecule Libraries