title: Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita.
abstract: In this study, we investigated global changes in miRNAs ofMeloidogyne incognitathroughout its life cycle. Small RNA sequencing resulted in approximately 62, 38, 38, 35, and 39 Mb reads in the egg, J2, J3, J4, and female stages, respectively. Overall, we identified 2724 known and 383 novel miRNAs (read count > 10) from all stages, of which 169 known and 13 novel miRNA were common to all the five stages. Among the stage-specific miRNAs, miR-286 was highly expressed in eggs, miR-2401 in J2, miR-8 and miR-187 in J3, miR-6736 in J4, and miR-17 in the female stages. These miRNAs are reported to be involved in embryo and neural development, muscular function, and control of apoptosis. Cluster analysis indicated the presence of 91 miRNA clusters, of which 36 clusters were novel and identified in this study. Comparison of miRNA families with other nematodes showed 17 families to be commonly absent in animal parasitic nematodes andM. incognita. Validation of 43 predicted common and stage-specific miRNA by quantitative PCR (qPCR) indicated their expression in the nematode. Stage-wise exploration ofM. incognitamiRNAs has not been carried out before and this work presents information on common and stage-specific miRNAs of the root-knot nematode.
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. parthi@chungbuk.ac.kr.
authors: Parthiban
authors: P
authors: Subramanian
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. inchchoi@korea.kr.
authors: In-Chan
authors: IC
authors: Choi
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. vimal@jbnu.ac.kr.|Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 761-756, Korea. vimal@jbnu.ac.kr.
authors: Vimalraj
authors: V
authors: Mani
authors: TheragenEtex Bio Institute, Gwanggyo-ro, Suwon 16229, Korea. jhpark98@gmail.com.
authors: Junhyung
authors: J
authors: Park
authors: TheragenEtex Bio Institute, Gwanggyo-ro, Suwon 16229, Korea. sathiya.moorthy@theragenetex.com.
authors: Sathiyamoorthy
authors: S
authors: Subramaniyam
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. hyuny24k@jbnu.ac.kr.|Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 761-756, Korea. hyuny24k@jbnu.ac.kr.
authors: Kang-Hyun
authors: KH
authors: Choi
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. jssim@korea.kr.
authors: Joon-Soo
authors: JS
authors: Sim
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. changmuk@korea.kr.
authors: Chang-Muk
authors: CM
authors: Lee
authors: Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 761-756, Korea. jkoo@jbnu.ac.kr.
authors: Ja Choon
authors: JC
authors: Koo
authors: Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea. bshahn@korea.kr.
authors: Bum-Soo
authors: BS
authors: Hahn
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D008018:Life Cycle Stages / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010063:Ovum / Q000254:growth & development / Q000378:metabolism; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid; D014431:Tylenchoidea / Q000235:genetics* / Q000254:growth & development
chemical_list: D035683:MicroRNAs; D018510:RNA, Helminth
keywords: Meloidogyne incognita; microRNA expression; quantitative polymerase chain reaction; stage-specific