title: Transcriptome-Wide Identification and Prediction of miRNAs and Their Targets in Paris polyphylla var. yunnanensis by High-Throughput Sequencing Analysis.
abstract: Long dormancy period of seeds limits the large-scale artificial cultivation of the scarceParis polyphyllavar.yunnanensis, an important traditional Chinese medicine. Characterizing miRNAs and their targets is crucial to understanding the role of miRNAs during seed dormancy in this species. Considering the limited genome information of this species, we first sequenced and assembled the transcriptome data of dormant seeds and their seed coats as the reference genome. A total of 146,671 unigenes with an average length of 923 bp were identified and showed functional diversity based on different annotation methods. Two small RNA libraries from respective seeds and seed coats were sequenced and the combining data indicates that 263 conserved miRNAs belonging to at least 83 families and 768 novel miRNAs in 1174 transcripts were found. The annotations of the predicted putative targets of miRNAs suggest that these miRNAs were mainly involved in the cell, metabolism and genetic information processing by direct and indirect regulation patterns in dormant seeds ofP. polyphyllavar.yunnanensis. Therefore, we provide the first known miRNA profiles and their targets, which will assist with further study of the molecular mechanism of seed dormancy inP. polyphyllavar.yunnanensis.
authors.affiliation: BGI-Yunnan, Kunming 650106, China. linglizhen@genomics.cn.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. linglizhen@genomics.cn.
authors.forename: Li-Zhen
authors.initials: LZ
authors.lastname: Ling
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China. sdchang@mail.kib.ac.cn.
authors.forename: Shu-Dong
authors.initials: SD
authors.lastname: Zhang
authors.affiliation: BGI-Yunnan, Kunming 650106, China. zhaofan@genomics.cn.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhao
authors.affiliation: BGI-Yunnan, Kunming 650106, China. Yangjinlong2@genomics.cn.
authors.forename: Jin-Long
authors.initials: JL
authors.lastname: Yang
authors.affiliation: BGI-Yunnan, Kunming 650106, China. songwenhui@genomics.cn.
authors.forename: Wen-Hui
authors.initials: WH
authors.lastname: Song
authors.affiliation: BGI-Yunnan, Kunming 650106, China. guanshenmin@genomics.cn.
authors.forename: Shen-Min
authors.initials: SM
authors.lastname: Guan
authors.affiliation: BGI-Yunnan, Kunming 650106, China. lixinshu@genomics.cn.
authors.forename: Xin-Shu
authors.initials: XS
authors.lastname: Li
authors.affiliation: BGI-Yunnan, Kunming 650106, China. huangzhuangjia@genomics.cn.
authors.forename: Zhuang-Jia
authors.initials: ZJ
authors.lastname: Huang
authors.affiliation: BGI-Yunnan, Kunming 650106, China. chengle@genomics.cn.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. chengle@genomics.cn.|College of Clinical Medicine, College of Basic Medical Sciences, Dali University, Dali 671000, China. chengle@genomics.cn.
authors.forename: Le
authors.initials: L
authors.lastname: Cheng
mesh_terms: D017124:Conserved Sequence / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D019668:Liliaceae / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Paris polyphylla var. yunnanensis; high-throughput sequencing technology; miRNAs; seed dormancy