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A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus
Zhang, Qi-Lin1,2; Zhang, Guan-Ling1; Yuan, Ming-Long3; Dong, Zhi-Xiang1; Li, Hong-Wei1; Guo, Jun1; Wang, Feng1; Deng, Xian-Yu1; Chen, Jun-Yuan (陈均远)2,4; Lin, Lian-Bing1
2018-12-18
发表期刊FRONTIERS IN PHYSIOLOGY
ISSN1664-042X
卷号9页码:13
摘要

Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belched + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (similar to 104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.

关键词Cephalochordata Amphioxus Phylogenomics Divergence History Speciation Process Protein Domains Evolutionary Genomics
DOI10.3389/fphys.2018.01833
语种英语
关键词[WOS]Asymmetron-lucayanum ; Molecular Evolution ; Absolute Rates ; Genome ; Model ; Times ; Transcriptome ; Annotation ; Sequences ; Orthologs
资助项目National Natural Science Foundation of China[31760042] ; National Natural Science Foundation of China[41272008] ; program B for Outstanding Ph.D. candidate of Nanjing University[201702B075]
WOS研究方向Physiology
WOS类目Physiology
WOS记录号WOS:000453704400001
项目资助者National Natural Science Foundation of China ; program B for Outstanding Ph.D. candidate of Nanjing University
出版者FRONTIERS MEDIA SA
文献类型期刊论文
条目标识符http://ir.nigpas.ac.cn/handle/332004/16183
专题中国科学院南京地质古生物研究所
其他
通讯作者Chen, Jun-Yuan (陈均远); Lin, Lian-Bing
作者单位1.Kunming Univ Sci & Technol, Fac Life Sci & Technol, Kunming, Yunnan, Peoples R China
2.Nanjing Univ, Sch Life Sci, Evodevo Inst, Nanjing, Jiangsu, Peoples R China
3.Lanzhou Univ, Coll Pastoral Agr Sci & Technol, State Key Lab Grassland Agroecosyst, Lanzhou, Gansu, Peoples R China
4.Chinese Acad Sci, Nanjing Inst Geol & Palaeontol, State Key Lab Palaeobiol & Stratig LPS, Nanjing, Jiangsu, Peoples R China
通讯作者单位中国科学院南京地质古生物研究所
推荐引用方式
GB/T 7714
Zhang, Qi-Lin,Zhang, Guan-Ling,Yuan, Ming-Long,et al. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus[J]. FRONTIERS IN PHYSIOLOGY,2018,9:13.
APA Zhang, Qi-Lin.,Zhang, Guan-Ling.,Yuan, Ming-Long.,Dong, Zhi-Xiang.,Li, Hong-Wei.,...&Lin, Lian-Bing.(2018).A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus.FRONTIERS IN PHYSIOLOGY,9,13.
MLA Zhang, Qi-Lin,et al."A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus".FRONTIERS IN PHYSIOLOGY 9(2018):13.
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