title: Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.
abstract: Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Shengfeng
authors.initials: S
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Zelin
authors.initials: Z
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Guangrui
authors.initials: G
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Qingyu
authors.initials: Q
authors.lastname: Yan
authors.affiliation: Evolution Biologique et Modélisation UMR 7353 Aix Marseille Université/CNRS, 3 Place Victor Hugo, 13331 Marseille, France.
authors.forename: Pierre Antoine
authors.initials: PA
authors.lastname: Pontarotti
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Hongchen
authors.initials: H
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Ruihua
authors.initials: R
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Tao
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Deng
authors.affiliation: 1] School of Life Sciences, Xiamen University, Xiamen 361005, China [2] Shenzhen Research Institute of Xiamen University, Shenzhen 518058, China.
authors.forename: Yiquan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 1] School of Life Sciences, Xiamen University, Xiamen 361005, China [2] Shenzhen Research Institute of Xiamen University, Shenzhen 518058, China.
authors.forename: Guang
authors.initials: G
authors.lastname: Li
authors.affiliation: Fujian Key Laboratory of Developmental and Neuron Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350108, China.
authors.forename: Qiujin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Sisi
authors.initials: S
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Leiming
authors.initials: L
authors.lastname: You
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Shaochun
authors.initials: S
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yonggui
authors.initials: Y
authors.lastname: Fu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Fenfang
authors.initials: F
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Meiling
authors.initials: M
authors.lastname: Dong
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Shangwu
authors.initials: S
authors.lastname: Chen
authors.affiliation: 1] State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China [2] Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing 100029, China.
authors.forename: Anlong
authors.initials: A
authors.lastname: Xu
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D005091:Exons; D016678:Genome; D064175:Lancelets / Q000145:classification / Q000235:genetics* / Q000502:physiology; D014714:Vertebrates / Q000145:classification / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements