title: Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa.
abstract: Despite modest sequence conservation and rapid evolution, long non-coding RNAs (lncRNAs) appear to be conserved in expression pattern and function. However, analysis of lncRNAs across tissues and developmental stages remains largely uncharacterized in mammals. Here, we systematically investigated the lncRNAs of the Guizhou miniature pig (Sus scrofa), which was widely used as biomedical model. We performed RNA sequencing across 9 organs and 3 developmental skeletal muscle, and developed a filtering pipeline to identify 10,813 lncRNAs (9,075 novel). Conservation patterns analysis revealed that 57% of pig lncRNAs showed homology to humans and mice based on genome alignment. 5,455 lncRNAs exhibited typical hallmarks of regulatory molecules, such as high spatio-temporal specificity. Notably, conserved lncRNAs exhibited higher tissue specificity than pig-specific lncRNAs and were significantly enriched in testis and ovary. Weighted co-expression network analysis revealed a set of conserved lncRNAs that are likely involved in postnatal muscle development. Based on the high degree of similarity in the structure, organization, and dynamic expression of pig lncRNAs compared with human and mouse lncRNAs, we propose that these lncRNAs play an important role in organ physiology and development in mammals. Our results provide a resource for studying animal evolution, morphological complexity, breeding, and biomedical research.
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
authors.forename: Zhonglin
authors.initials: Z
authors.lastname: Tang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yu-Cheng T
authors.initials: YT
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Zishuai
authors.initials: Z
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Jiapei
authors.initials: J
authors.lastname: Yuan
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Chaoju
authors.initials: C
authors.lastname: Hua
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Xinhao
authors.initials: X
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Guanglin
authors.initials: G
authors.lastname: Niu
authors.affiliation: Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
authors.forename: Yubo
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Zhi John
authors.initials: ZJ
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
authors.forename: Kui
authors.initials: K
authors.lastname: Li
mesh_terms: D000825:Animal Structures; D000818:Animals; D000831:Animals, Newborn; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D062085:RNA, Long Noncoding / Q000096:biosynthesis*; D017423:Sequence Analysis, RNA; D017385:Sequence Homology; D062211:Spatio-Temporal Analysis; D013552:Swine / Q000235:genetics* / Q000254:growth & development*
chemical_list: D062085:RNA, Long Noncoding