title: Low diversity, activity, and density of transposable elements in five avian genomes.
abstract: In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Gao
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Saisai
authors.initials: S
authors.lastname: Wang
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Yali
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Shen
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Songlei
authors.initials: S
authors.lastname: Xue
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Cai
authors.initials: C
authors.lastname: Chen
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
authors.forename: Hengmi
authors.initials: H
authors.lastname: Cui
authors.affiliation: Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China. cysong@yzu.edu.cn.
authors.forename: Chengyi
authors.initials: C
authors.lastname: Song
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D004251:DNA Transposable Elements; D016678:Genome; D010802:Phylogeny; D011110:Polymorphism, Genetic; D018626:Retroelements
chemical_list: D004251:DNA Transposable Elements; D018626:Retroelements
keywords: Activity; Avian; Diversity; Genome size; Transposable elements