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Mob DNA. 2019 May 6;10:19. doi: 10.1186/s13100-019-0161-8. eCollection 2019.

Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs.

Author information

1
1Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China.
2
2Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
3
3Life Science Center, University of Missouri, Columbia, MO 65211 USA.
4
4Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Abstract

Background:

Retrotransposons are the major determinants of genome sizes and they have shaped both genes and genomes in mammalian organisms, but their overall activity, diversity, and evolution dynamics, particularly their impact on protein coding and lncRNA genes in pigs remain largely unknown.

Results:

In the present study, we performed de novo detection of retrotransposons in pigs by using multiple pipelines, four distinct families of pig-specific L1 s classified into 51 distinct subfamilies and representing four evolution models and three expansion waves of pig-specific SINEs represented by three distinct families were identified. ERVs were classified into 18 families and found two most "modern" subfamilies in the pig genome. The transposition activity of pig L1 was verified by experiment, the sense and antisense promoter activities of young L1 5'UTRs and ERV LTRs and expression profiles of young retrotransposons in multiple tissues and cell lines were also validated. Furthermore, retrotransposons had an extensive impact on lncRNA and protein coding genes at both the genomic and transcriptomic levels. Most protein coding and lncRNA (> 80%) genes contained retrotransposon insertions, and about half of protein coding genes (44.30%) and one-fourth (24.13%) of lncRNA genes contained the youngest retrotransposon insertions. Nearly half of protein coding genes (43.78%) could generate chimeric transcripts with retrotransposons. Significant distribution bias of retrotransposon composition, location, and orientation in lncRNA and protein coding genes, and their transcripts, were observed.

Conclusions:

In the current study, we characterized the classification and evolution profile of retrotransposons in pigs, experimentally proved the transposition activity of the young pig L1 subfamily, characterized the sense and antisense expression profiles and promoter activities of young retrotransposons, and investigated their impact on lncRNA and protein coding genes by defining the mobilome landscapes at the genomic and transcriptomic levels. These findings help provide a better understanding of retrotransposon evolution in mammal and their impact on the genome and transcriptome.

KEYWORDS:

Distribution bias; Gene overlapping; Pig genome; Promoter activity; Retrotransposition activity; Retrotransposon evolution

Conflict of interest statement

Animal care and use was approved by the Animal Care and Use Committee of Yangzhou University.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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