title: Identification and characterization of the miRNA transcriptome of Ovis aries.
abstract: The discovery and identification of Ovis aries (sheep) miRNAs will further promote the study of miRNA functions and gene regulatory mechanisms. To explore the microRNAome (miRNAome) of sheep in depth, samples were collected that included eight developmental stages: the longissimus dorsi muscles of Texel fetuses at 70, 85, 100, 120, and 135 days, and the longissimus dorsi muscles of Ujumqin fetuses at 70, 85, 100, 120, and 135 d, and lambs at 0 (birth), 35, and 70 d. These samples covered all of the representative periods of Ovis aries growth and development throughout gestation (about 150 d) and 70 d after birth. Texel and Ujumqin libraries were separately subjected to Solexa deep sequencing; 35,700,772 raw reads were obtained overall. We used ACGT101-miR v4.2 to analyze the sequence data. Following meticulous comparisons with mammalian mature miRNAs, precursor hairpins (pre-miRNAs), and the latest sheep genome, we substantially extended the Ovis aries miRNAome. The list of pre-miRNAs was extended to 2,319, expressing 2,914 mature miRNAs. Among those, 1,879 were genome mapped to unique miRNAs, representing 2,436 genome locations, and 1,754 pre-miRNAs were mapped to chromosomes. Furthermore, the Ovis aries miRNAome was processed using an elaborate bioinformatic analysis that examined multiple end sequence variation in miRNAs, precursors, chromosomal localizations, species-specific expressions, and conservative properties. Taken together, this study provides the most comprehensive and accurate exploration of the sheep miRNAome, and draws conclusions about numerous characteristics of Ovis aries miRNAs, including miRNAs and isomiRs.
authors.affiliation: National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Shifang
authors.initials: S
authors.lastname: Zhang
authors.forename: Fuping
authors.initials: F
authors.lastname: Zhao
authors.forename: Caihong
authors.initials: C
authors.lastname: Wei
authors.forename: Xihui
authors.initials: X
authors.lastname: Sheng
authors.forename: Hangxing
authors.initials: H
authors.lastname: Ren
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.forename: Jian
authors.initials: J
authors.lastname: Lu
authors.forename: Jiasen
authors.initials: J
authors.lastname: Liu
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.forename: Lixin
authors.initials: L
authors.lastname: Du
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D014644:Genetic Variation; D035683:MicroRNAs / Q000235:genetics*; D009132:Muscles / Q000378:metabolism; D011247:Pregnancy; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D034561:Sheep, Domestic / Q000235:genetics* / Q000254:growth & development; D014960:X Chromosome / Q000235:genetics
chemical_list: D035683:MicroRNAs