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complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis

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Zoological Research 2018年第2期39卷 127-129页

作者： chatmongkon suwannapoom ya-jiang wu xing chen adeniyi c.adeola jing chen wen-zhi wang school of agriculture and natural resources university of phayaoPhayao 56000Thailand southeast asia biodiversity research institute(cas-seabri) chinese academy of sciencesYezin Nay Pyj Taw 05282Myanmar state key laboratory for conservation and utilization of bio-resource in yunnan yunnan universityKunming Yunnan 650091china state key laboratory of genetic resources and evolution kunming institute of zoologychinese academy of sciencesKunming Yunnan 650223China wildlife forensics science service centre Kunming Yunnan 650203China guizhou academy of testing and analysis guizhou academy of sciencesGuiyang Guizhou 550002China

DEAR EDITOR,In this study, we sequenced the complete mitochondrial genome （mitogenome） of the Thai Red Junglefowl （RJF; Gallus gallus） using the next-generation sequencing （NGS） platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, chiang Mai Province, northern Thailand Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% c, and 13.5% G, resulting in a high percentage of A＋T （50.4%）. Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as ＇data deficient＇ in Thailand.

关键词： mtDNA complete mitochondrial genome of the Thai Red Junglefowl Gallus gallus

Artificial selection drives differential gene expression during pig domestication

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Journal of Genetics and Genomics 2019年第2期46卷 97-100页

作者： Yang Yang chaorui Liu adeniyi c.adeola Xierzhatijiang Sulaiman Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming college of Life Science University of Chinese Academy of Sciences National Pilot School of Software Yunnan University college of Uighur Medicine Xinjiang Medical University

Domestication of livestock involves drastic phenotypic changes driven by strong artificial selection,such as tame behavior and coat *** abundant phenotypic variations established during animal domestication have provi... 详细信息

关键词： ASE FST ADP SLc cWB PPARD AWB cis

capture Probe: a java tool for designing probes for capture Hi-c applications

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Zoological Research 2020年第1期41卷 94-96页

作者： Yun-Fei Ma adeniyi cadeola Yan-Bo Sun Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming college of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of chinese Academy of Sciences Beijing 100049China State Key Laboratory for conservation and Utilization of Bio-resource and Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan ProvinceYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory *** Hi-c is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic *** can identify interactions among target loci and all other loci in a genome with low cost and high ***,we developed captureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or *** parameters helped to achieve and optimize the designed *** testing of captureProbe showed high efficiency in the design success ratio of target loci and probe ***,this program will help scientists conduct genome spatial interaction research.

关键词： capture EDIT Probe

Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 423-436页

作者： Jianbo Li Ligang Wang Dawei Yu Junfeng Hao Longchao Zhang adeniyi c.adeola Bingyu Mao Yun Gao Shifang Wu chunling Zhu Yongqing Zhang Jilong Ren changgai Mu David M.Irwin Lixian Wang Tang Hai Haibing Xie Yaping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China State Key Laboratory of Stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China core Facility for Protein Research Institute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory for Molecular and Developmental Biology CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Kunming college of Life Science University of Chinese Academy of SciencesKunming 650223China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoOntario M5S1A8Canada center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Development of thoracolumbar vertebra(TLV)and rib primordium(RP)is a common evolutionary feature across vertebrates,although whole-organism analysis of the expression dynamics of TLV-and RP-related genes has been ***,we investigated the single-cell transcriptome landscape of thoracic vertebra(TV),lumbar vertebra(LV),and RP cells from a pig embryo at 27 days post-fertilization(dpf)and identified six cell types with distinct gene expression ***-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP *** analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA103′-UTR sequence specific to osteoblasts of LV cells,which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV ***,this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution,which serves as a comprehensive view on the transcriptional profile of animal embryo development.

关键词： scRNA-seq Thoracolumbar vertebra transition Rib-genesis Osteogenesis Angiogenesis

Associations of autozygosity with economic important traits in a cross of Eurasian pigs

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Journal of Genetics and Genomics 2023年第3期50卷 216-220页

作者： Lin Tao Li-Gang Wang adeniyi c.adeola Long-chao Zhang Lian-Wei Li Qing-Long Li Dao-Ji cen chen Yan Zhan-Shan Ma Li-Xian Wang Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution&Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming college of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China computational Biology and Medical Ecology Lab State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China State Key Laboratory for conservation and Utilization of Bioresource in Yunnan School of Life ScienceYunnan UniversityKunmingYunnan 650091China

Inbreeding depression(ID)refers to the undesirable effects of inbreeding(mating of relatives)on fitness-associated phenotypes(charlesworth and Willis,2009).ID on production,reproduction,and health traits is relevant to industrial profitability,making it important in animal *** of homozygosity(ROH)is a good measure of inbreeding and autozygosity(the inheritance of two copies of an ancestral allele)(Alkuraya,2013).

关键词： Eurasian profit reproduction

ABcc4 abnormal caused preaxial polydactyly in pigs by disrupting ciliogenesis

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ABCC4 abnormal caused preaxial polydactyly in pigs by disrup...

OrthReg:a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

2018中国遗传学会第十次全国会员代表大会暨学术讨论会

作者： cheng Ma Xuman Han Saber Khederzadeh adeniyi c.adeola Haibing Xie Yaping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of Sciences Kunming college of Life Science University of Chinese Academy of Sciences University of chinese Academy of Sciences

Polydactyly is the most common congenital limb dysplasia in many species. Its formation is related to multiple genes but the molecular mechanism of this malformation has not yet been accurately studied. Here we reported a preaxial polydactyly（PPD） family in Large White pigs with 3 affected and 13 unaffected individuals and another random PPD case, and identified candidate loci causing PPD with whole genome resequencing strategies. The current results revealed that the PPD phenotype has strong association with variations of ABcc4（ATP-binding cassette sub-family c member 4）, a gene encoding a transmembrane protein involved in ciliogenesis. Haplotype analysis showed that the affected individuals shared long stretches of haplotypes at the ABcc4. A missense mutation（I85 T） in ABcc4 was identified in a highly conserved protein domain and showed a high level of differentiation between the affected and unaffected pigs. Moreover, the results found that earlier reported genes were not associated with the PPD phenotypes in two studied pig populations. Our results emphasized a role of ciliogenesis in PPD formation and provided a new candidate gene for PPD investigation.

关键词： Preaxial polydactyly ABcc4 ciliogenesis SHH

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Zoological Research 2020年第4期41卷 471-475页

作者： Yun-Fei Ma cui-Ping Huang Fang-Ru Lu Jin-Xiu Li Xu-Man Han adeniyi cadeola Yun Gao Jia-Kun Deng Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming college of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of chinese Academy of Sciences Beijing100049China center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China State Key Laboratory for conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province School of Life SciencesYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENcODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG consortium et al., 2015)offer pioneering data on regulatory elements in several species. currently, however, regulatory element annotation data remain limited for most organisms.

关键词： species. traits regulatory

Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones

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current Zoology 2019年第6期65卷 713-724页

作者： Lotanna M.NNEJI adeniyi c.adeola Fang YAN Agboola O.OKEYOYIN Ojo c.OLADIPO Yohanna SAIDU Dinatu SAMUEL Ifeanyi c.NNEJI Akindele O.ADEYI Abiodun B.ONADEKO Temidayo E.OLAGUNJU Olatunde OMOTOSO Segun O.OLADIPO Oluyinka A.IYIOLA John Y.USONGO Timothy AUTA Abbas D.USMAN Halima ABDULLAHI Odion O.IKHIMIUKOR Wei-Wei ZHOU Jie-Qiong JIN Obih A.UGWUMBA Adiaha A.A.UGWUMBA Min-Sheng PENG Robert W.MURPHY Jing cHE State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Sino-Africa Joint Research center Chinese Academy of SciencesKunming 650223China National Park Service Headquarters Federal Capital TerritoryAbuja 900001Nigeria Old Oyo National Park Oyo State 211242Nigeria Gashaka Gumti National Park SertiTaraba State 663101Nigeria Department of Biological Sciences University of AbujaFCTAbuja 902101Nigeria Department of Zoology University of IbadanIbadanOyo State 200284Nigeria Department of Zoology University of LagosLagos 100213Nigeria Department of Biosciences and Biotechnology Kwara State UniversityMaleteKwara State 241104Nigeria Department of Zoology Faculty of Life SciencesUniversity of llorinllorinKwara State 240103Nigeria Department of Zoology Modibbo Adama University of TechnologyYola 640101Nigeria Department of Biological Sciences Federal University Dutsin-MaKatsina State 821Nigeria Department of Biology Kashim Ibrahim College of EducationMaiduguriBorno State 600230Nigeria Department of Microbiology University of IbadanIbadanOyo State 200284Nigeria centre for Biodiversity and conservation Biology Royal Ontario MuseumTorontoOntarioCanada M5S 2C6

Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic *** its vertebrate fauna,reptiles have broad distributions,thus,they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species *** red-headed rock agama,Agama agama,lives in a wide range of habitats and,thus,it may show genetic structuring and ***,we tested the hypothesis that ecology affects its genetic structure and population *** inference phylogenetic analysis of a mitochondrial DNA(mtDNA)gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic *** differences among populations based on the mtDNA also correlated with geographic distance. The ecologicalniche model for the matrilines had a good fit and robust performance. Population divergence alongthe environmental axes was associated with climatic conditions, and temperature ranked highestamong all environmental variables for forest specialists, while precipitation ranked highest for theforest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that nicheconservatism promotes geographic isolation of the western populations of Nigerian A. ***, ecological gradients and geographic isolation impact the genetic structure and population divergenceof the lizards. This species might be facing threats due to recent habitat fragmentation,especially in western Nigeria. conservation actions appear necessary.

关键词： Agama agama ecological speciation genogeography Nigeria population divergence vegetation

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非洲珍珠鸡的遗传多样性及环境适应

非洲珍珠鸡的遗传多样性及环境适应