title: Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing.
abstract: MicroRNAs play important regulatory roles in eukaryotic lineages. In this paper, we employed deep sequencing technology to sequence and identify microRNAs in M. incognita genome, which is one of the important plant parasitic nematodes. We identified 102 M. incognita microRNA genes, which can be grouped into 71 nonredundant miRNAs based on mature sequences. Among the 71 miRANs, 27 are known miRNAs and 44 are novel miRNAs. We identified seven miRNA clusters in M. incognita genome. Four of the seven clusters, miR-100/let-7, miR-71-1/miR-2a-1, miR-71-2/miR-2a-2 and miR-279/miR-2b are conserved in other species. We validated the expressions of 5 M. incognita microRNAs, including 3 known microRNAs (miR-71, miR-100b and let-7) and 2 novel microRNAs (NOVEL-1 and NOVEL-2), using RT-PCR. We can detect all 5 microRNAs. The expression levels of four microRNAs obtained using RT-PCR were consistent with those obtained by high-throughput sequencing except for those of let-7. We also examined how M. incognita miRNAs are conserved in four other nematodes species: C. elegans, A. suum, B. malayi and P. pacificus. We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans. Our research created a unique resource for the research of plant parasitic nematodes. The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.
authors.affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China; Institute of Vegetables and Flowers, CAAS, Beijing, PR China.
authors.forename: Yunsheng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, CAAS, Beijing, PR China.
authors.forename: Zhenchuan
authors.initials: Z
authors.lastname: Mao
authors.affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China.
authors.forename: Jin
authors.initials: J
authors.lastname: Yan
authors.affiliation: College of Life Sciences, Beijing Normal University, Beijing, PR China.
authors.forename: Xinyue
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Institute of Vegetables and Flowers, CAAS, Beijing, PR China.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China.
authors.forename: Luo
authors.initials: L
authors.lastname: Xiao
authors.affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China.
authors.forename: Liangying
authors.initials: L
authors.lastname: Dai
authors.affiliation: School of Computing, Clemson University, Clemson, South Carolina, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Luo
authors.affiliation: Institute of Vegetables and Flowers, CAAS, Beijing, PR China.
authors.forename: Bingyan
authors.initials: B
authors.lastname: Xie
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics; D001483:Base Sequence; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling; D015801:Helminth Proteins / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018510:RNA, Helminth / Q000235:genetics*; D034741:RNA, Small Interfering; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014431:Tylenchoidea / Q000235:genetics* / Q000254:growth & development
chemical_list: D060565:Argonaute Proteins; D018076:DNA, Complementary; D015801:Helminth Proteins; D035683:MicroRNAs; D018510:RNA, Helminth; D034741:RNA, Small Interfering