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Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

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Zoological Research 2023年第1期44卷 20-29页

作者： Hojjat Asadollahpour Nanaei yudong cai Akil Alshawi Jiayue Wen Tanveer Hussain Wei-Wei Fu Nai-Yi Xu Abdulameer Essa Johannes ALenstra Xihong Wang Yu Jiang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China Department of Internal and Preventive Medicine College of Veterinary MedicineUniversity of BaghdadIraqi Ministry of Higher Education and Scientific ResearchBagdad 10090Iraq Department of Molecular Biology Virtual University of PakistanLahore 54000Pakistan Animal Genetics Resources Department Directorate of Animal Resourcesthe Ministry of Iraqi AgricultureBaghdad 10081Iraq Faculty of Veterinary Medicine Utrecht University3508 TD UtrechtThe Netherlands

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated wholegenome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient(Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia(SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex(C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.

关键词： Goat Adaptation KITLG Southwest Asia Nubian ibex

GGVD:A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

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Journal of Genetics and Genomics 2021年第3期48卷 248-256页

作者： Weiwei Fu Rui Wang Jiantao Yu Dexiang Hu yudong cai Junjie Shao Yu Jiang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China College of Information Engineering Northwest A&F UniversityYanglingShaanxi 712100China

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data.With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples,a user-friendly database making efficient reuse of these important resources is needed.Here,we use the genomes of 208 modern domestic goats,24 bezoars,46 wild ibexes,and 82 ancient goats to present a comprehensive goat genome variation database(GGVD).GGVD hosts a total of~41.44 million SNPs,~5.14 million indels,6,193 selected loci,and 112 introgression regions.Users can freely visualize the frequency of genomic variations in geographical maps,selective sweeps in interactive tables,Manhattan plots,or line charts,as well as the heatmap patterns of the SNP genotype.Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early,middle,and late stages.For facilitating access to sequence features,the UCSC Genome Browser,BLAT,BLAST,Lift Over,and pcadapt are also integrated into GGVD.GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs,and it is publicly available at http://***/Goat Var.

关键词： Goat Genetic structure Variation Selective signature Introgression Database

盐度超敏感离子水凝胶的制备及其在可视化盐度检测和智能液体阀上的应用

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Science China Materials 2024年第1期67卷 321-330页

作者：闫小草师琪蔡玉东佟亚轩吴继红翁云宣高海南 College of Chemistry and Materials Engineering Beijing Technology and Business UniversityBeijing 100048China Synthetic Resin Laboratory Petrochemical Research InstitutePetrochinaBeijing 102206China

对超低浓度盐溶液响应产生大尺度形变的功能水凝胶在海水渗透能收集、刺激响应分离材料、智能传感和致动器等方面具有广阔的应用前景.本文结合聚电解质和两性离子聚合物开发了一种盐度超敏感离子水凝胶.以稀盐作为分散介质时,水凝胶体... 详细信息

对超低浓度盐溶液响应产生大尺度形变的功能水凝胶在海水渗透能收集、刺激响应分离材料、智能传感和致动器等方面具有广阔的应用前景.本文结合聚电解质和两性离子聚合物开发了一种盐度超敏感离子水凝胶.以稀盐作为分散介质时,水凝胶体积缩小为原来1/60.本文研究了盐响应水凝胶的溶胀、形态和力学性能,并基于拉曼光谱对聚合物网络盐响应重构行为进行了表征.此外,利用毛细管和盐响应水凝胶成功设计了一种可视化、便携离子检测计,可媲美商用水质监测计.同时开发了具有传感和致动功能的智能液阀,用于自动感应调节液体的流出和输送.该盐敏感水凝胶在淡水监测和调控、海水渗透能收集、刺激响应分离材料、智能软机器人和电子穿戴等方面具有很大的应用潜力.

关键词：智能传感聚合物网络水凝胶自动感应机器人分离材料离子检测聚电解质

山羊P2RY12-P2RY13单倍型渗入鉴定及其功能分析

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家畜生态学报 2024年第1期45卷 9-15页

作者：刘晓懿蔡钰东郑惠玲姜雨西北农林科技大学动物科技学院陕西杨凌712100

基因渗入对动物的驯化以及适应性的提高起到了至关重要的作用。该研究收集了世界范围内共163只现代家山羊、81只古代家山羊以及69只山羊野生近缘种的基因组数据,进行全基因组遗传变异检测、构建Neighbor-joining树、单倍型网络图以及蛋... 详细信息

基因渗入对动物的驯化以及适应性的提高起到了至关重要的作用。该研究收集了世界范围内共163只现代家山羊、81只古代家山羊以及69只山羊野生近缘种的基因组数据,进行全基因组遗传变异检测、构建Neighbor-joining树、单倍型网络图以及蛋白质结构预测。我们发现家山羊基因组chr1:116312 kb~116397 kb区域内存在来自阿尔卑斯北山羊或伊比利亚北山羊的渗入。这段长达85 kb的渗入单倍型包含2个与乳腺炎相关的蛋白编码基因P2RY12和P2RY13,其中P2RY12基因上来自渗入单倍型的变异Pro317Ser导致了蛋白质末端α-螺旋的增长,该渗入单倍型主要存在于欧洲和非洲的现代家山羊群体中,频率分别为52.1%和32.1%。通过对古代样本进行分析,推测该单倍型的渗入最早发生于3000 a前的欧洲地区,可能由于对泌乳性状的选择而导致其频率升高并扩散至非洲地区。该研究为家山羊基因组中P2RY12-P2RY13单倍型的来源与功能提供了新的见解。

关键词：山羊渗入基因组古代DNA

Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

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Science China(Life Sciences) 2020年第5期63卷 750-763页

作者： Xiaomeng Tian Ran Li Weiwei Fu Yan Li Xihong Wang Ming Li Duo Du Qianzi Tang yudong cai Yiming Long Yue Zhao Mingzhou Li Yu Jiang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Institute of Animal Genetics and Breeding College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China

Pigs were domesticated independently in the Near East and China,indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide.Therefore,12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome.As a result,72.5 Mb of nonredundant sequences(~3% of the genome)were found to be absent from the reference genome(Sscrofa11.1)and were defined as pan-sequences.Of the pan-sequences,9.0 Mb were dominant in Chinese pigs,in contrast with their low frequency in European pigs.One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3(TIG3)gene which is involved in fatty acid metabolism.Using flanking sequences and Hi-C based methods,27.7% of the sequences could be anchored to the reference genome.The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure.A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

关键词： pan-genome pig reference genome 3D chromatin structure presence-absence variation

A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication

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Science China(Life Sciences) 2021年第7期64卷 1116-1130页

作者： Ran Li Peng Yang Ming Li Wenwen Fang Xiangpeng Yue Hojjat Asadollahpour Nanaei Shangquan Gan Duo Du yudong cai Xuelei Dai Qimeng Yang Chunna Cao Weidong Deng Sangang He Wenrong Li Runlin Ma Mingjun Liu Yu Jiang Key Laboratory ofAnimal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China State Key Laboratory of Grassland Agro-ecosystems Key Laboratory of Grassland Livestock Industry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland IndustryMinistry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730020China State Key Laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural and Reclamation SciencesShihezi 832000China Faculty of Animal Science and Technology Yunan Agricultural UniversityKunming 650201China Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock Ministry of AgricultureAnimal Biotechnology Research InstituteXinjiang Academy of Animal ScienceUrumqi 830026China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages.Here,we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome(o MSY),using nanopore sequencing and Hi-C technologies.The o MSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons.Three major paternal lineages(HY1a,HY1b and HY2)were defined across domestic sheep,of which HY2 was newly detected.Surprisingly,HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b.Demographic analysis of Y chromosomes,mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep,the wild mouflons in Southeastern Anatolia.Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.

关键词： Y chromosome sheep paternal lineage introgression de novo assembly

A novel voting system for the identification of eukaryotic genome promoters

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Journal of Biomedical Science and Engineering 2010年第7期3卷 719-726页

作者： Lin Lei Kaiyan Feng Zhisong He yudong cai 不详

Motivation: Accurate identification and delineation of promoters/TSSs (transcription start sites) is important for improving genome annotation and devising experiments to study and understand transcriptional regulation. Many promoter identifiers are developed for promoter identification. However, each promoter identifier has its own focuses and limitations, and we introduce an integration scheme to combine some identifiers together to gain a better prediction performance. Result: In this contribution, 8 promoter identifiers (Proscan, TSSG, TSSW, FirstEF, eponine, ProSOM, EP3, FPROM) are chosen for the investigation of integration. A feature selection method, called mRMR (Minimum Redundancy Maximum Relevance), is novelly transferred to promoter identifier selection by choosing a group of robust and complementing promoter identifiers. For comparison, four integration methods (SMV, WMV, SMV_IS, WMV_IS), from simple to complex, are developed to process a training dataset with 1400 se- quences and a testing dataset with 378 sequences. As a result, 5 identifiers (FPROM, FirstEF, TSSG, epo- nine, TSSW) are chosen by mRMR, and the integration of them achieves 70.08% and 67.83% correct prediction rates for a training dataset and a testing dataset respectively, which is better than any single identifier in which the best single one only achieves 59.32% and 61.78% for the training dataset and testing dataset respectively.

关键词： MRMR (Minimum Redundancy Maximum Relevance) Transcription Start Sites (TSS) Promoter Identification Promoter Identifier Integration

Predicting DNA methylation status using word composition

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Journal of Biomedical Science and Engineering 2010年第7期3卷 672-676页

作者： Lingyi Lu Kao Lin Ziliang Qian Haipeng Li yudong cai Yixue Li 不详

Background: DNA methylation will influence the gene expression pattern and cause the changes of the genetic functions. Computational analysis of the methylation status for nucleotides can help to explore the underlying reasons for developing methylations. Results: We present a DNA sequence based method to analyze the methylation status of CpG dinucleotides using 5bp (5-mer) DNA fragments – named as the word composition encoding method. The prediction accuracy is 75.16% when all 5bp word compositions are used (totally 45 = 1024). Furthermore, 5-bp DNA fragments/words having the most impact on the methylation status are identified by mRMR (Maximum-Relevant-Minimum-Redundancy) feature selection method. As a result, 58 words are selected, and they are used to build a compact predictor, which achieves 77.45% prediction accuracy. When the word composition encoding method and the feature selection strategy are coupled together, the meaning of these words can be analyzed through their contribution towards the prediction. The biological evidence in the literature supports that the surrounding DNA sequence of the CpG dinucleotides will affect the methylation of the CpG dinucleotides. Conclusions: The main contribution of this paper is to find out and analyze the key DNA words taken from the neighbor-hood of the CpG dinucleotides that are inducing the DNA methylation.

关键词： Feature Selection MRMR 5bp Nucleotide Fragment Nearest Neighbor Algorithm

An atlas of CNV maps in cattle, goat and sheep

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Science China(Life Sciences) 2021年第10期64卷 1747-1764页

作者： Yongzhen Huang Yunjia Li Xihong Wang Jiantao Yu yudong cai Zhuqing Zheng Ran Li Shunjin Zhang Ningbo Chen Hojjat Asadollahpour Nanaei Quratulain Hanif Qiuming Chen Weiwei Fu Chao Li Xiukai Cao Guangxian Zhou Shudong Liu Sangang He Wenrong Li Yulin Chen Hong Chen Chuzhao Lei Mingjun Liu Yu Jiang College of Animal Science and Technology Northwest A&F UniversityYangling 712100China College of Information Engineering Northwest A&F UniversityYangling 712100China Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock Ministry of AgricultureBiotechnology Research InstituteXinjiang Academy of Animal SciencesUrumqi 830026China National Institute for Biotechnology and Genetic Engineering(NIBGE) Faisalabad 577PunjabPakistan Pakistan Institute of Engineering&Applied Sciences(PIEAS) Nilore 45650IslamabadPakistan

Copy number variation(CNV)is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans,animals and plants.However,the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown.Here,we generated CNV region(CNVR)datasets which were diverged or shared among cattle,goat,and sheep,including 886 individuals from 171 diverse populations.Using 9 environmental factors for genome-wide association study(GWAS),we identified a series of candidate CNVRs,including genes relating to immunity,tick resistance,multi-drug resistance,and muscle development.The number of CNVRs shared between species is significantly higher than expected(P<0.00001),and these CNVRs may be more persist than the single nucleotide polymorphisms(SNPs)shared between species.We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes.This study provides the evidence that balancing selection might be more common in mammals than previously considered,and might play an important role in the daily activities of these ruminant species.

关键词： copy number variation species-shared balancing selection ruminant livestock