High-throughput sequencing and degradome analysis reveal neutral evolution of Cercis gigantea microRNAs and their targets.
High-throughput sequencing and degradome analysis for Cercis gigantea identified 194 known miRNAs and 23 novel miRNAs with 61 targets. The comparison results of highly conserved miRNAs and non-conserved miRNAs implied that C. gigantea miRNAs were subjected to the neutral evolution. MicroRNAs play a key role in post-transcriptionally regulating gene expression during plant growth, development and other various biological processes. Although numerous miRNAs have been identified and documented, to date, there are no reports on Cercis gigantea (C. gigantea) miRNAs. In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among these, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. The comparison results revealed that highly conserved miRNAs have higher expression levels, more family members and more targets than non-conserved miRNAs, indicating that C. gigantea miRNAs were subjected to the neutral evolution. Meanwhile, these conserved miRNAs were also found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes, which will help further understanding regulatory mechanisms of C. gigantea miRNAs.
School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China. gwn0807@shu.edu.cn.
Wenna
W
Guo
Yangzhou Breeding Biological Agriculture Technology Co. Ltd, Yangzhou, 225200, People's Republic of China. zhyingfly@163.com.
Ying
Y
Zhang
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, People's Republic of China. Wangq@nju.edu.cn.
Qiang
Q
Wang
School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China. zhanyp@shu.edu.cn.
Yueping
Y
Zhan
School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China. moonshadowzhu@gmail.com.
Guanghui
G
Zhu
Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China. yuphar@126.com.|Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China. yuphar@126.com.|Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China. yuphar@126.com.
Qi
Q
Yu
School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China. zhuliucun1983@163.com.
Liucun
L
Zhu
D001483:Base Sequence; D004722:Endoribonucleases; D007887:Fabaceae / Q000235:genetics*; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D040961:Genetic Drift; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D035683:MicroRNAs / Q000235:genetics*; D009097:Multienzyme Complexes; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D018547:Plant Stems / Q000235:genetics; D011117:Polyribonucleotide Nucleotidyltransferase; D020365:RNA Helicases; D012323:RNA Processing, Post-Transcriptional; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA
D035683:MicroRNAs; D009097:Multienzyme Complexes; D018749:RNA, Plant; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D020365:RNA Helicases
Degradome analysis; High-throughput sequencing; Legume; Neutral evolution; miRNA