The Bama Xiang pig (BMX) Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and Eas...The Bama Xiang pig (BMX) Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.展开更多
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. ...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.展开更多
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 t...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 management.Runs of homozygosity(ROH)is a good measure of inbreeding and autozygosity(the inheritance of two copies of an ancestral allele)(Alkuraya,2013).展开更多
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 lack...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 lacking.Here,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 signatures.In-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP development.Further 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 transition.Thus,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.展开更多
Domestication of livestock involves drastic phenotypic changes driven by strong artificial selection,such as tame behavior and coat color.These abundant phenotypic variations established during animal domestication ha...Domestication of livestock involves drastic phenotypic changes driven by strong artificial selection,such as tame behavior and coat color.These abundant phenotypic variations established during animal domestication have provided valuable resources to study the evolutionary mechanisms underlying domestication.展开更多
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA(mt DNA) D...Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA(mt DNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups(matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf(Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1(but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.展开更多
Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism.Among its vertebrate fauna,reptiles have broad distributions,thus,they constitute a compelling system for asse...Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism.Among 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 diversification.The red-headed rock agama,Agama agama,lives in a wide range of habitats and,thus,it may show genetic structuring and diversification.Herein,we tested the hypothesis that ecology affects its genetic structure and population divergence.Bayesian inference phylogenetic analysis of a mitochondrial DNA(mtDNA)gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions.Genetic 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. agama.Thus, 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.展开更多
基金supported by grants from the National Natural Science Foundation of China(31472000)National 973 Program of China(2013CB835203)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘The Bama Xiang pig (BMX) Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
基金supported by the National Key Research and Development Program(2016YFC1200705)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01:2015CASEABR1002)+2 种基金Ministry of Science and Technology of China(2012FY110800)Chinese Academy of Sciences(KFZD-SW-208)Yunnan Provincial Science and Technology Department
文摘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.
基金supported by the National Key Research and Development Program of China(2021YFF1000602)the Chinese Academy of Sciences(XDA24010107)+2 种基金the National Natural Science Foundation of China(31750110480)the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(the Large Research Infrastructure Funding)the Spring City Plan:the High-level Talent Promotion and Training Project of Kunming(2022SCP001)。
文摘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 management.Runs of homozygosity(ROH)is a good measure of inbreeding and autozygosity(the inheritance of two copies of an ancestral allele)(Alkuraya,2013).
基金This work was supported by the Strategic Pioneer Program of the Chinese Academy of Sciences(Grant No.XDA24010107)the Ministry of Agriculture of China(Grant No.2016ZX08009003-006)+2 种基金the China Agriculture Research System(Grant No.CARS-35)the Agricultural Science and Technology Innovation Project,China(Grant No.ASTIP-IAS02)This work was supported by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(the Large Research Infrastructure Funding).
文摘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 lacking.Here,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 signatures.In-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP development.Further 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 transition.Thus,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.
基金supported by the grants from the Chinese Academy of Sciences (XDA08010304)the National Natural Science Foundation of China (31472000)+1 种基金the Ministry of Agriculture of China (2016ZX08009003-006)the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding)
文摘Domestication of livestock involves drastic phenotypic changes driven by strong artificial selection,such as tame behavior and coat color.These abundant phenotypic variations established during animal domestication have provided valuable resources to study the evolutionary mechanisms underlying domestication.
基金supported by Sino-Africa Joint Research Center, Chinese Academy of Sciences (Nos. SAJC201611 and SAJC201306)the National Basic Research program (Nos. 2013CB835200 and 2013CB835202)+3 种基金The Youth Innovation Promotion Association, Chinese Academy of Sciences, provided support to M.S.P. and G.D.W.supported by the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding)supported, in part, by a Visiting Professorship for Senior International Scientists from the Chinese Academy of Sciencesmanuscript preparation by a Natural Sciences and Engineering Research Council of Canada Discovery Grant A3148 to R.W.M
文摘Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA(mt DNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups(matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf(Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1(but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
文摘Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism.Among 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 diversification.The red-headed rock agama,Agama agama,lives in a wide range of habitats and,thus,it may show genetic structuring and diversification.Herein,we tested the hypothesis that ecology affects its genetic structure and population divergence.Bayesian inference phylogenetic analysis of a mitochondrial DNA(mtDNA)gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions.Genetic 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. agama.Thus, 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.