A5102995722- Genetic and phenotypic traits in livestock
- Congenital limb and hand anomalies
- Genomic variations and chromosomal abnormalities
- Hedgehog Signaling Pathway Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Metabolomics and Mass Spectrometry Studies
- Genomics and Chromatin Dynamics
- High Altitude and Hypoxia
- Animal Genetics and Reproduction
- Genetic and Kidney Cyst Diseases
- Wildlife Ecology and Conservation
- Genetic Syndromes and Imprinting
- melanin and skin pigmentation
- Animal Disease Management and Epidemiology
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- interferon and immune responses
- RNA Research and Splicing
- Congenital heart defects research
- Genetic diversity and population structure
- Metallurgy and Material Science
- Antimicrobial Peptides and Activities
- Prion Diseases and Protein Misfolding
- vaccines and immunoinformatics approaches
Chinese Academy of Sciences
2015-2025
Kunming Institute of Zoology
2015-2025
University of Chinese Academy of Sciences
2019-2023
University of Surrey
2020
Instituto de Ciencias Agrarias
2020
Yunnan University
2008
Abstract Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs dogs at both high low altitudes, including 73 generated this study, to disentangle mechanisms underlying local adaptation of mammals. Although molecular convergence is comparatively rare DNA sequence level, found convergent signature positive selection gene particularly...
Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations increase runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand genetic underpinnings depression. Here we integrated comprehensive dataset comprising 7239 domesticated wild boars genotyped by single nucleotide polymorphism (SNP) chips, along phenotypic data encompassing growth, reproduction...
Abstract Tibetan pig is native to the Qinghai-Tibet Plateau and has adapted high-altitude environmental condition such as hypoxia. However, its origin genetic mechanisms underlying adaptation still remain controversial enigmatic. Herein, we analyze 229 genomes of wild domestic pigs from Eurasia, including 63 pigs, detect 49.6 million high-quality variants. Phylogenomic structure analyses show that have a close relationship with low-land in China, implying common domestication origin....
African wild suids consist of several endemic species that represent ancient members the family Suidae and have colonized diverse habitats on continent. However, limited genomic resources for hinder our understanding their evolution genetic diversity. In this study, we assembled high-quality genomes a common warthog (Phacochoerus africanus), red river hog (Potamochoerus porcus), as well an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed diverged from ancestor...
Abstract Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize methylation pattern pig lincRNA genes in adipose and muscle tissues. Our study showed that level was higher than mRNA genes, with similar trends observed comparisons promoter, exon or intron regions. Different were across transcription start sites (TSS) protein-coding genes....
A common phenotypic difference among domestic animals is variation in coat color. Six-white-point a pigmentation pattern observed varying pig breeds, which seems to have evolved through several different mechanistic pathways. Herein, we re-sequenced whole genomes of 31 Diannan small-ear pigs from China and found that the six-white-point color likely regulated by polygenic loci, rather than MC1R locus. Strong associations were at three loci (EDNRB, CNTLN, PINK1), explain about 20 percent...
The Bama Xiang pig (BMX) is a famous early-maturing Chinese indigenous breed with two-end black coat. To uncover the genetic basis of BMX phenotype, we conducted comparative genomic analyses between and East Asian wild boars Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated gonadal hormone melanin synthesis, consistent phenotypic changes observed during development pigs. We also performed differentially expressed gene analysis based on RNA-seq data...
The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after last ice age. Here we present first analysis SNP polymorphism within complete mtDNA genome West Russian (n = 8), 64), and North African 5) boar. Our analyses provided evidence unique lineages in East-Caucasian (Dagestan) region Central Italy. A phylogenetic revealed that these are basal to other sequences. We also show close connection between Western...
http://www.ibiomedical.net/pigvar/.
Development of thoracolumbar vertebra (TLV) and rib primordium (RP) is a common evolutionary feature across vertebrates, although whole-organism analysis the expression dynamics TLV- RP-related genes has been lacking. Here, we investigated single-cell transcriptome landscape thoracic (TV), lumbar (LV), RP cells from pig embryo at 27 days post-fertilization (dpf) identified six cell types with distinct gene signatures. In-depth dissection RNA velocity revealed coupled process osteogenesis...
The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved the determination coat color. We investigated diversity Nigerian indigenous (NIP) by simultaneously analyzing variation mitochondrial DNA (mtDNA), Y-chromosome sequence melanocortin receptor 1 (MC1R) gene. Median-joining network analysis mtDNA D-loop sequences 201 NIP...
Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in advanced stages speciation, genetics isolation nascent stage speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying early great details. Pig breeds not evolved large X-effect hybrid incompatibility commonly observed between "good species." Instead, deleterious epistatic...
Abstract Background Polydactyly is one of the most common congenital limb dysplasia in many animal species. Although preaxial polydactyly (PPD) has been comprehensively studied humans as a abnormality, genetic variations other species have not fully understood. Herein, we focused on pig, an even-toed ungulate mammal model with its unique advantages medical and researches, two PPD families consisting four affected 20 normal individuals were sequenced. Results Our results showed that sampled...
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF pig-producing regions country. To facilitate control, it important to understand genotype phylogenetic relationship viruses (ASFVs). Recent genetic analysis ASFV isolates has revealed presence both genotypes I II; this based on few selected genes. Phylogenetic whole...
Abstract Solar energy, which is essential for the origin and evolution of all life forms on Earth, can be objectively recorded through attributes such as climatic ambient temperature (CAT), ultraviolet radiation (UVR), sunlight duration (SD). These have specific geographical variations may cause different adaptation traits. However, profile each attribute selective role solar energy a whole during human remain elusive. Here, we performed genome-wide study with respect to CAT, UVR, SD using...
Abstract Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution genetic convergence. Here, we utilized 327 genomes from horses, sheep, goats, cattle, pigs dogs at both high low altitudes, including 73 generated this study, to disentangle mechanisms underlying local adaptation of mammals. Although molecular convergence is comparatively rare DNA sequence level, found convergent signature positive selection gene...
The authors declare no conflict of interest. final ancestral sequences in FASTA (https://doi.org/10.57760/sciencedb.07853), the multi-genome alignment HAL (https://doi.org/10.57760/sciencedb.07855) and states all Sscrofa11.1 positions validated by re-sequencing data (https://doi.org/10.57760/sciencedb.07858) are accessible at ScienceDB. Appendix S1 S2 Please note: publisher is not responsible for content or functionality any supporting information supplied authors. Any queries (other than...
Abstract Background Many conserved secondary structures have been identified within elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations these populations and their biological functions not fully studied. Results We searched for polymorphisms number SNPs even though they highly among species. density is about 65% that flanking, non-conserved, sequences. Classification sites as stems or loops/bulges revealed 62% found...