Publications by authors named "Yan-Hu Liu"

17 Publications

  • Page 1 of 1

Whole-genome sequencing reveals lactase persistence adaptation in European dogs.

Mol Biol Evol 2021 Jul 20. Epub 2021 Jul 20.

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, 650223, China.

Coexistence and cooperation between dogs and humans over thousands of years have supported convergent evolutionary processes in the two species. Previous studies found that Eurasian dogs evolved into a distinct geographic cluster. In this study, we used the genomes of 242 European dogs, 38 Southeast Asian indigenous dogs (SEAI) and 41 grey wolves to identify adaptation of European dogs. We report 86 unique positively selected genes (PSGs) in European dogs, among which is LCT (lactase). LCT encodes lactase which is fundamental for the digestion of lactose. We found that an A-to-G mutation (chr19:38,609,592) is almost fixed in Middle Eastern and European dogs. The results of 2 D SFS support that the mutation is under soft sweep. We inferred that the onset of positive selection of the mutation is shorter than 6,535 years and behind the well-developed dairy economy in central Europe. It increases the expression of LCT by reducing its binding with ZEB1, which would enhance dog's ability to digest milk-based diets. Our study uncovers the genetic basis of convergent evolution between humans and dogs with respect to diet, emphasizing the import of the dog as a bio-medical model for studying mechanisms of the digestive system.
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http://dx.doi.org/10.1093/molbev/msab214DOI Listing
July 2021

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome.

Genes (Basel) 2021 May 30;12(6). Epub 2021 May 30.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named "Tasha" initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.
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http://dx.doi.org/10.3390/genes12060847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8228171PMC
May 2021

863 genomes reveal the origin and domestication of chicken.

Cell Res 2020 08 25;30(8):693-701. Epub 2020 Jun 25.

Department of Animal Science, Iowa State University, Ames, IA, USA.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.
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http://dx.doi.org/10.1038/s41422-020-0349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395088PMC
August 2020

Genomic regions under selection in the feralization of the dingoes.

Nat Commun 2020 02 3;11(1):671. Epub 2020 Feb 3.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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http://dx.doi.org/10.1038/s41467-020-14515-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997406PMC
February 2020

Interspecific Gene Flow Shaped the Evolution of the Genus Canis.

Curr Biol 2018 11 18;28(21):3441-3449.e5. Epub 2018 Oct 18.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim, Norway.

The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.
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http://dx.doi.org/10.1016/j.cub.2018.08.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224481PMC
November 2018

Selection and environmental adaptation along a path to speciation in the Tibetan frog .

Proc Natl Acad Sci U S A 2018 05 14;115(22):E5056-E5065. Epub 2018 May 14.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;

Tibetan frogs, , are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including in the brain, and in the heart, and in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.
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http://dx.doi.org/10.1073/pnas.1716257115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984489PMC
May 2018

PigVar: a database of pig variations and positive selection signatures.

Database (Oxford) 2017 01;2017

State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

Database Url: http://www.ibiomedical.net/pigvar/.
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http://dx.doi.org/10.1093/database/bax048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502369PMC
January 2017

Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites.

Mol Biol Evol 2018 02;35(2):287-298

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and School of Life Sciences, Yunnan University, Kunming, Yunnan, China.

Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88-3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.
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http://dx.doi.org/10.1093/molbev/msx258DOI Listing
February 2018

Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome.

Sci Rep 2016 10 7;6:35004. Epub 2016 Oct 7.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.

Genome-wide studies on high-altitude adaptation have received increased attention as a classical case of organismal evolution under extreme environment. However, the current genetic understanding of high-altitude adaptation emanated mainly from autosomal analyses. Only a few earlier genomic studies paid attention to the allosome. In this study, we performed an intensive scan of the X chromosome of public genomic data generated from Tibetan Mastiff (TM) and five other dog populations for indications of high-altitude adaptation. We identified five genes showing signatures of selection on the X chromosome. Notable among these genes was angiomotin (AMOT), which is related to the process of angiogenesis. We sampled additional 11 dog populations (175 individuals in total) at continuous altitudes in China from 300 to 4,000 meters to validate and test the association between the haplotype frequency of AMOT gene and altitude adaptation. The results suggest that AMOT gene may be a notable candidate gene for the adaptation of TM to high-altitude hypoxic conditions. Our study shows that X chromosome deserves consideration in future studies of adaptive evolution.
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http://dx.doi.org/10.1038/srep35004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054530PMC
October 2016

Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation.

Nat Genet 2016 08 11;48(8):947-52. Epub 2016 Jul 11.

San Diego Zoo Institute for Conservation Research, Escondido, California, USA.

The snub-nosed monkey genus Rhinopithecus includes five closely related species distributed across altitudinal gradients from 800 to 4,500 m. Rhinopithecus bieti, Rhinopithecus roxellana, and Rhinopithecus strykeri inhabit high-altitude habitats, whereas Rhinopithecus brelichi and Rhinopithecus avunculus inhabit lowland regions. We report the de novo whole-genome sequence of R. bieti and genomic sequences for the four other species. Eight shared substitutions were found in six genes related to lung function, DNA repair, and angiogenesis in the high-altitude snub-nosed monkeys. Functional assays showed that the high-altitude variant of CDT1 (Ala537Val) renders cells more resistant to UV irradiation, and the high-altitude variants of RNASE4 (Asn89Lys and Thr128Ile) confer enhanced ability to induce endothelial tube formation in vitro. Genomic scans in the R. bieti and R. roxellana populations identified signatures of selection between and within populations at genes involved in functions relevant to high-altitude adaptation. These results provide valuable insights into the adaptation to high altitude in the snub-nosed monkeys.
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http://dx.doi.org/10.1038/ng.3615DOI Listing
August 2016

Out of southern East Asia: the natural history of domestic dogs across the world.

Cell Res 2016 Jan 15;26(1):21-33. Epub 2015 Dec 15.

State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.
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http://dx.doi.org/10.1038/cr.2015.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816135PMC
January 2016

DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues.

Sci Rep 2015 Oct 23;5:15435. Epub 2015 Oct 23.

State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components of genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize the DNA methylation pattern of pig lincRNA genes in adipose and muscle tissues. Our study showed that the methylation level of lincRNA genes was higher than that of mRNA genes, with similar trends observed in comparisons of the promoter, exon or intron regions. Different methylation pattern were observed across the transcription start sites (TSS) of lincRNA and protein-coding genes. Furthermore, an overlap was observed between many lincRNA genes and differentially methylated regions (DMRs) identified among different breeds of pigs, which show different fat contents, sexes and anatomic locations of tissues. We identify a lincRNA gene, linc-sscg3623, that displayed differential methylation levels in backfat between Min and Large White pigs at 60 and 120 days of age. We found that a demethylation process occurred between days 150 and 180 in the Min and Large White pigs, which was followed by remethylation between days 180 and 210. These results contribute to our understanding of the domestication of domestic animals and identify lincRNA genes involved in adipogenesis and muscle development.
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http://dx.doi.org/10.1038/srep15435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616017PMC
October 2015

DoGSD: the dog and wolf genome SNP database.

Nucleic Acids Res 2015 Jan 17;43(Database issue):D777-83. Epub 2014 Nov 17.

Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼ 19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies.
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http://dx.doi.org/10.1093/nar/gku1174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383968PMC
January 2015

Balancing selection on CDH2 may be related to the behavioral features of the Belgian Malinois.

PLoS One 2014 10;9(10):e110075. Epub 2014 Oct 10.

State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

The Belgian Malinois (BM) is an excellent working dog that typically shows a circling behavior when placed in a confined space. Moreover, individuals showing moderate running in circles (one kind of obsessive compulsive behavior) in confined spaces typically show better work performance compared to those without the circling behavior or to those with a serious circling behavior (which can be defined as an obsessive compulsive disorder (OCD)). To determine whether the candidate gene CDH2, Cadherin 2, which is associated with OCD in the Doberman pinscher breed of dogs and in humans, was linked with this behavioral character in the BM, population genetic analyses were performed on a BM population and a natural population of the Chinese indigenous dog (CID). Many genetic signals of balancing selection were detected for one specific region of the CDH2 gene, which suggests that a genomic block, which is included in the CDH2 gene, experienced balancing selection in the BM, and that the CDH2 gene might be associated with the behavioral characteristics of the BM dog (a balance between circling behavior and work performance). Moreover one specific variant, G63913941A, which creates a predicted transcription factor-binding site, may be the key mutation in the CDH2 gene affecting the behavior of BMs by allowing the binding of a transcription factor and increasing CDH2 expression.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110075PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193869PMC
December 2015

Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.

Genome Biol Evol 2014 Jun 2;6(6):1387-92. Epub 2014 Jun 2.

Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, ChinaState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaLaboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in the human and mouse genomes, some of which play important roles in fundamental biological processes. The pig is an important domesticated animal, however, pig lincRNAs remain poorly characterized and it is unknown if they were involved in the domestication of the pig. Here, we used available RNA-seq resources derived from 93 samples and expressed sequence tag data sets, and identified 6,621 lincRNA transcripts from 4,515 gene loci. Among the identified lincRNAs, some lincRNA genes exhibit synteny and sequence conservation, including linc-sscg2561, whose gene neighbor Dnmt3a is associated with emotional behaviors. Both linc-sscg2561 and Dnmt3a show differential expression in the frontal cortex between domesticated pigs and wild boars, suggesting a possible role in pig domestication. This study provides the first comprehensive genome-wide analysis of pig lincRNAs.
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http://dx.doi.org/10.1093/gbe/evu113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079208PMC
June 2014