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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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Wang Y, Zhan H, Zhang Y, Long Z, Yang X. Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae). Biodivers Data J 2023; 11:e101942. [PMID: 38327340 PMCID: PMC10848841 DOI: 10.3897/bdj.11.e101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/11/2023] [Indexed: 02/09/2024] Open
Abstract
Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.
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Affiliation(s)
- Yeying Wang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Haofeng Zhan
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Yu Zhang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Zhengmin Long
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Xiaofei Yang
- Guizhou University, Guiyang, ChinaGuizhou UniversityGuiyangChina
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3
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Li X, Wang X, Yang C, Lin L, Yuan H, Lei F, Huang Y. A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation. Integr Zool 2023; 18:225-236. [PMID: 36049502 DOI: 10.1111/1749-4877.12673] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Tibetan Partridge (Perdix hodgsoniae) is an endemic species distributed in high-altitude areas of 3600-5600 m on the Qinghai-Tibet Plateau. To explore how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17 457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus), and Mikado Pheasant (Syrmaticus mikado). We found that 1014, 2595, and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs, respectively, of which 965 genes were common under positive selection with 3 different programs. Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while 6 gene families were under contraction. The total number of olfactory receptor genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on the evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engeering, Xi'an University, Xi'an, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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4
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Ma X, Li J, Chen B, Li X, Ling Z, Feng S, Cao S, Zuo Z, Deng J, Huang X, Cai D, Wen Y, Zhao Q, Wang Y, Zhong Z, Peng G, Jiang Y, Gu Y. Analysis of microbial diversity in the feces of Arborophila rufipectus. Front Microbiol 2023; 13:1075041. [PMID: 36817108 PMCID: PMC9932278 DOI: 10.3389/fmicb.2022.1075041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/31/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Intestinal microbiota composition plays a crucial role in modulating the health of the host. This evaluation indicator is very sensitive and profoundly impacts the protection of endangered species. Currently, information on the gut microbiota of wild birds remains scarce. Therefore, this study aimed to describe the gut microbial community structure and potentially, the pathogen composition of wild Arborophila rufipectus. Methods To guarantee comprehensive data analysis, we collected fecal samples from wild A. rufipectus and Lophura nycthemera in their habitats for two quarters. The 16S rRNA gene was then sequenced using high-throughput sequencing technology to examine the intestinal core microbiota, microbial diversity, and potential pathogens with the aim of determining if the composition of the intestinal microflora varies seasonally. Results and Discussion The gut microbiota of A. rufipectus and L. nycthemera primarily comprised four phyla: Proteobacteria (45.98%), Firmicutes (35.65%), Bacteroidetes (11.77%), and Actinobacteria (3.48%), which accounted for 96.88% of the total microbial composition in all samples. At the genus level, core microorganisms were found, including Shigella (10.38%), Clostridium (6.16%), Pseudomonas (3.03%), and Rickettsiella (1.99%). In these genera, certain microbial species have been shown to be pathogenic. This study provides important indicators for analyzing the health status of A. rufipectus and formulating protective measures.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Junshu Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Benping Chen
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Xinni Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhenwen Ling
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Shenglin Feng
- Authority of Administration, Sichuan Laojunshan National Nature Reserve, Yibin, China
| | - Sanjie Cao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhicai Zuo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Junliang Deng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dongjie Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiping Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guangneng Peng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaozhang Jiang
- Department of Bioengineering, Sichuan Water Conservancy Vocational College, Chengdu, China,*Correspondence: Yaozhang Jiang, ; Yu Gu,
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China,*Correspondence: Yaozhang Jiang, ; Yu Gu,
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5
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Yu J, Liu J, Li C, Wu W, Feng F, Wang Q, Ying X, Qi D, Qi G. Characterization of the complete mitochondrial genome of Otus lettia: exploring the mitochondrial evolution and phylogeny of owls (Strigiformes). Mitochondrial DNA B Resour 2021; 6:3443-3451. [PMID: 34805524 PMCID: PMC8604474 DOI: 10.1080/23802359.2021.1995517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Large-scale molecular phylogenetic studies of the avian order Strigiformes have been performed, and numerous mitochondrial genomes have been determined. However, their intergeneric relationships are still controversial, and few comprehensive comparative analyses of mitochondrial genomes have been conducted on Strigiformes. In this study, the mitochondrial genome of Otus lettia was determined and compared with other Strigiformes. The O. lettia mitochondrial genome was 16,951 bp in size. For Strigiformes, atp8 can be used as a suitable molecular marker for population genetic diversity, while cox1 is a candidate barcoding marker for species identification. All protein-coding genes may be under strong purifying selection pressure, and one extra cytosine insertion located in nad3 is common to all owls except Tyto longimembris, T. alba, and Athene noctua. Four different mitochondrial gene arrangement types were found among the Strigiformes mitogenomes, and their evolutionary relationship between each other can be perfectly explained by the tandem duplication and random loss model. The phylogenetic topologies using the mitochondrial genomes showed that target species O. lettia had a closer relationship with O. scops + O. sunia than O. bakkamoena, the genus Glaucidium was paraphyletic, and the Ninox clade was located at the basal position of Strigidae lineage. Our phylogenetic trees also supported the previous recommendations that Sceloglaux albifacies, Ciccaba nigrolineata, and Ketupa flavipes should be transferred to Ninox, Strix, and Bubo, respectively. These findings will be helpful in further unraveling the mitochondrial evolution and phylogeny of Strigiformes.
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Affiliation(s)
- Jiaojiao Yu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Jiabin Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Cheng Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Wei Wu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Feifei Feng
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Qizhi Wang
- Sichuan Nanshan Forestry Judicial Appraisal Center, Chengdu, China
| | - Xiaofeng Ying
- Sichuan Nanshan Forestry Judicial Appraisal Center, Chengdu, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Guilan Qi
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
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6
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Tian Y, Xu J, Dou L, Zheng A, Qiao L, Xie J, Zhang X. The complete mitochondrial genome of Indian Cuckoo Cuculus micropterus (Aves: Cuculiformes). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2556-2558. [PMID: 34377828 PMCID: PMC8330708 DOI: 10.1080/23802359.2021.1959461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Indian Cuckoo, Cuculus micropterus, belongs to the family Cuculidae. In this paper, we sequenced and analysized the complete mitochondrial genome of C. micropterus. The complete mitochondrial genome of C. micropterus is 17,541 bp in length, which was submitted to the NCBI database under the accession number MZ048030. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA is 33.2% for A, 24.2% for T, 29.8% for C, and 12.8% for G, with a GC content of 42.6%. In order to explore the molecular phylogenetics evolution of Cuculidae, the nucleotide sequence data of 13 PCGs of C. micropterus and other 11 Cuculiformes were used for the phylogenetic analysis. The result shows that C. micropterus is closely related to Cuculus canorus bakeri. The study contributes to illuminating the taxonomic status of C. micropterus, and may facilitate further investigation of the evolution of Cuculidae.
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Affiliation(s)
- Yu'ang Tian
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Jingtong Xu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Liang Dou
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Anqin Zheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Lu Qiao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Jiqin Xie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, PR China
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7
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Xia S, Qiao L, Yang K, Yue B, Yang N. The complete mitochondrial genome of Robin Accentor Prunella rubeculoides (Passeriformes: Prunellidea). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3676-3677. [PMID: 33367056 PMCID: PMC7646584 DOI: 10.1080/23802359.2020.1832596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we determined and described the complete mitochondrial genome of Robin Accentor (Prunella rubeculoides), the first complete mitogenome. The complete genome of P. rubeculoides was 16,796 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA was 29.7% for A, 23.7% for T, 15.6% for G, and 31.0% for C, with a GC content of 46.6%. This information of P. rubeculoides mitogenome is significance for phylogenetic studies of the family Prunellidea.
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Affiliation(s)
- Shan Xia
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Lu Qiao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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8
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Chen D, Liu Y, Davison G, Yong DL, Gao S, Hu J, Li SH, Zhang Z. Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences. Mol Phylogenet Evol 2020; 151:106895. [PMID: 32562823 DOI: 10.1016/j.ympev.2020.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/06/2020] [Accepted: 06/12/2020] [Indexed: 11/18/2022]
Abstract
The advent of the phylogenomic era has significantly improved our understanding of the evolutionary history and biogeography of Southeast Asia's diverse avian fauna. However, the taxonomy and phylogenetic relationships of many Southeast Asian birds remain poorly resolved, especially for those with large geographic ranges, which might have experienced both ancient and recent geological and environmental changes. In this study, we examined the evolutionary history and biogeography of the hill partridges (Galliformes: Phasianidae: Arborophila spp.), currently the second most speciose galliform genus, and thought to have colonized Southeast Asia from Africa. We present a well-resolved phylogeny of 14 Arborophila species inferred from ultra-conserved elements, exons, and mitochondrial genomes from both fresh and museum samples, which representing almost complete coverage of the genus. Our fossil-calibrated divergence time estimates and biogeographic modeling showed the ancestor of Arborophila arrived in Indochina during the early Miocene, but the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification within Arborophila were driven by several tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling and extensive dispersal and speciation of Sundaic Arborophila during the Pleistocene sea-level fluctuations. Taken together, these results suggest that the evolutionary history and biogeography of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Geoffrey Davison
- National Biodiversity Centre, National Parks Board, 1 Cluny Road, 259569, Singapore
| | - Ding Li Yong
- BirdLife International (Asia), 354 Tanglin Road, #01-16/17, Tanglin International Centre, Singapore 247672, Singapore; Fenner School of Environment and Society, The Australian National University, Linnaeus Way, Canberra, ACT 2601, Australia
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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9
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Yang N, Wu Y, Qiao L, Zhao D, Yang K. The complete mitochondrial genome of Black-streaked Scimitar Babbler Pomatorhinus dedekeni (Passeriformes: Timaliidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1731339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, P. R. China
| | - Yong Wu
- Xuebaoding National Nature Reserve Administration, Pingwu, P. R. China
| | - Lu Qiao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Ding Zhao
- Xuebaoding National Nature Reserve Administration, Pingwu, P. R. China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, P. R. China
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10
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Genome-wide investigation of microsatellite polymorphism in coding region of the giant panda (Ailuropoda melanoleuca) genome: a resource for study of phenotype diversity and abnormal traits. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00418-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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12
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Xu Y, Li W, Hu Z, Zeng T, Shen Y, Liu S, Zhang X, Li J, Yue B. Genome-wide mining of perfect microsatellites and tetranucleotide orthologous microsatellites estimates in six primate species. Gene 2017; 643:124-132. [PMID: 29223358 DOI: 10.1016/j.gene.2017.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/16/2022]
Abstract
Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r=0.310, p=0.550), and were positively correlated with the total length of SSRs (Pearson, r=0.992, p=0.00). A total of 224,289 tetranucleotide orthologous microsatellites families and 367 single-copy orthologous SSRs loci were found in six primate species by homologous alignment. The inner mutation types of single-copy orthologous SSRs loci included the copy number variance, point mutation, and chromosomal translocation. The accumulated repeat times and average length of tetranucleotide orthologous microsatellites in Rhinopithecus roxellana, Papio anubis and Macaca mulatta were longer than Homo sapiens and Pan troglodytes, which showed the tetranucleotide orthologous SSRs loci had more repeat times and longer average length on the branches with earlier divergence time, one exception may be Microcebus murinus as a primitive monkey with a smallest morphology in Malagasy. Our conclusion indicated that single-copy tetranucleotide orthologous SSRs sequences accumulated individual mutation more slowly through time in H. sapiens and P. troglodytes than in R. roxellanae, P. anubis and M. mulatta. However, such divergence wouldn't arise uniformly in all branches of the primate tree. A comparison of genomic sequence assemblages would offer remarkable insights about comparisons and contrasts, and the evolutionary processes of the microsatellites involved in human and nonhuman primate species.
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Affiliation(s)
- Yongtao Xu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Zongxiu Hu
- Yibin Hengshu Animal Models Resource Industry Technology Academy, Yibin 644609, PR China
| | - Tao Zeng
- Yibin Hengshu Animal Models Resource Industry Technology Academy, Yibin 644609, PR China
| | - Yongmei Shen
- Sichuan Engineering Research Center for Medical Animal, Chengdu 610064, PR China
| | - Sanxu Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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