Sheep is an important livestock species raised globally to produce meat,milk,wool,and other by-products.During the Neolithic Revolution,sheep were domesticated in the Fertile Crescent of Southwest Asia around 10,000 y...Sheep is an important livestock species raised globally to produce meat,milk,wool,and other by-products.During the Neolithic Revolution,sheep were domesticated in the Fertile Crescent of Southwest Asia around 10,000 years ago(Chessa et al.,2009).展开更多
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes...Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools.The catalytic properties of all enzymes are primarily dictated by their structures,which are predominantly determined by their amino acid sequences.However,this aspect has not been fully considered in the enzyme bioprospecting processes.With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts,structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties.Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise.Here,we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates,in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.展开更多
Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demon...Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.展开更多
The timing and location of chicken(Gallus gallus domesticus)domestication have remained controversial for over a century[1].Several researchers have proposed China as one of the early centers for chicken domestication...The timing and location of chicken(Gallus gallus domesticus)domestication have remained controversial for over a century[1].Several researchers have proposed China as one of the early centers for chicken domestication[2].This is based on a few archaeological‘‘chicken"remains discovered in China(Table S1).Recently,one investigation detected mitochondrial DNA(mt DNA)haplotypes展开更多
Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau ...Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.展开更多
文摘Sheep is an important livestock species raised globally to produce meat,milk,wool,and other by-products.During the Neolithic Revolution,sheep were domesticated in the Fertile Crescent of Southwest Asia around 10,000 years ago(Chessa et al.,2009).
基金Funding was provided by the Agricultural Biotechnology Research Institute of Iran(ABRII),Swedish Research Council(Vetenskapsrådet grant no.:2017-05019)the BBSRC Institute Strategic Programme Gut Microbes and Health(BB/r012490/1,its constituent project BBS/e/F/000Pr10355).
文摘Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools.The catalytic properties of all enzymes are primarily dictated by their structures,which are predominantly determined by their amino acid sequences.However,this aspect has not been fully considered in the enzyme bioprospecting processes.With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts,structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties.Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise.Here,we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates,in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
基金supported by the National Natural Science Foundation of China(31621062)Strategic Priority Research Program of the Chinese Academy of Sciences(XDA2004010302)+4 种基金Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK05010703)supported by the National Natural Science Foundation of China(91731304,31822048)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB13020600)Qinghai Department of Science and Technology Major ProjectState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan,Yunnan University(2018KF001)supported by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
基金supported by Guangdong Natural Science Foundation(2014A030307018)Science&Technology Planning Project of Guangdong Province(2015A020208020,2016A030303068)+2 种基金Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01:2015CASEABRI002)the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of SciencesThe Institute of Animals for Scientific Purpose Development(IAD)provided permission(U1-01205-2558)in Thailand
文摘The timing and location of chicken(Gallus gallus domesticus)domestication have remained controversial for over a century[1].Several researchers have proposed China as one of the early centers for chicken domestication[2].This is based on a few archaeological‘‘chicken"remains discovered in China(Table S1).Recently,one investigation detected mitochondrial DNA(mt DNA)haplotypes
基金supported by the Tibetan R&D Program,China(Grant No.XZ202101ZD0001N)the China Agriculture Research System(Grant No.CARS-39)the National Natural Science Foundation of China(Grant Nos.31900313,32161143010,and 31972526).
文摘Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.
