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Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

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Journal of Animal Science and Biotechnology 2024年第1期15卷 88-107页

作者： Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang Chongqing Academy of Animal Science Rongchang DistrictChongqing 402460China Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and Rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Chongqing Engineering Research Center of Goose Genetic Improvement Rongchang DistrictChongqing 402460China Department of Cardiovascular Ultrasound and Non‑Invasive Cardiology Sichuan Academy of Medical Sciences and Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu611731China Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province University of Electronic Science and Technology of ChinaChengdu611731China JiguangGene Biotechnology Co. Ltd.Nanjing210032China Jiangsu Agri-Animal Vocational College Taizhou225300China Poultry Science Institute Chongqing Academy of Animal ScienceNo.51 Changzhou AvenueRongchang DistrictChongqing 402460P.R.China

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic *** a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic *** To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq *** constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose ***,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among ***-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition *** instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique ***,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild *** study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple orga

关键词： Gene-CDS haplotype Goose GWAS pan-genome Presence-absence variation Selection signal

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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 ***,12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference *** 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 *** the pan-sequences,9.0 Mb were dominant in Chinese pigs,in contrast with their low frequency in European *** sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3(TIG3)gene which is involved in fatty acid *** flanking sequences and Hi-C based methods,27.7% of the sequences could be anchored to the reference *** 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

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High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

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Plant Communications 2022年第6期3卷 235-250页

作者： Changyou Liu Yan Wang Jianxiang Peng Baojie Fan Dongxu Xu Jing Wu Zhimin Cao Yunqing Gao Xueqing Wang Shutong Li Qiuzhu Su Zhixiao Zhang Shen Wang Xingbo Wu Qibing Shang Huiying Shi Yingchao Shen Bingbing Wang Jing Tian Institute of Cereal and Oil Crops Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and BreedingShijiazhuang 050035China Biobin Data Sciences Changsha 410221China Zhangjiakou Academy of Agricultural Sciences Zhangjiakou 075300China Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081China Tropical Research and Education Center Department of Environmental HorticultureUniversity of Florida18905 SW 280th StHomesteadFL 33031USA

Mung bean is an economically important legume crop species that is used as a food,consumed as a vegetable,and used as an ingredient and even as a *** explore the genomic diversity of mung bean,we assembled a high-quality reference genome(Vrad_JL7)that was479.35 Mb in size,with a contig N50 length of 10.34 Mb.A total of 40,125 protein-coding genes were annotated,representing96.9%of the genetic *** also sequenced 217 accessions,mainly landraces and cultivars from China,and identified 2,229,343 high-quality single-nucleotide polymorphisms(SNPs).Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese *** diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk *** constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference *** the genes,83.1%were core genes and 16.9%were ***/absence variation(PAV)events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the *** association studies(GWASs)revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits,including a SNP in the coding region of the SWEET10 homolog(jg24043)involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related *** high-quality reference genome and pan-genome will provide insights into mung bean breeding.

关键词： mung bean long-read sequencing de novo assembly pan-genome gene PAV GWAS

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pan-genome:a new sight for bacterial genome dynamics

Pan-genome:a new sight for bacterial genome dynamics

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Yongbing Zhao Junhui Yang Jiayan Wu Jingfa Xiao CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences Graduate School of Chinese Academy of Sciences

The reducing cost of DNA sequencing and the increasing number of bacterial genome sequences have provided a chance to study the profile and evolution of microbial genome from population ***-genome,the genetic repertoire of a given species,comprises three parts including core genome,dispensable genome and strains-specific *** genome represents those genes shared by all strains,and these genes are mainly responsible for basic process of life and species major *** genome includes those genes shared by two or more,but not all strains,and strains-specific genome are genes shared by only one *** general,dispensable genes and strain-specific genes function in contribute to the species diversity and selective advantages,such as adaptation to different niche and antibiotic resistance or colonization of a new host,and sometimes strains-specific genes are related to *** the pan-genome was present in Streptococcus agalactiae genome analysis for the first time,pan-genome analysis was employed in more than forty-three bacterial species or ***,the key issue for pangenome analysis is how to select appropriate mathematical models to depict the bacterial pan-genome feature and detect homologs(gene or genome region) from multiple genome *** algorithms and pipelines were designed to identify orthologs genes and homologs regions from multiple species,such as inparanoid/multiparanoid,Mauve,PGAP and so *** pan-genome profile was indicated from the relationship between the strains number and new detected genes,strains specific genes and the whole gene pool size under various mathematical *** important aspect is to combine specific problems in biology with pan-genome *** these years,pan-genome analysis has shed a new sight into the dynamic variation of bacterial genes composition during differentiation and adaption to different niche,and facilitated the identification of strain-specific features,s

关键词： pan-genome genome dynamics adaption evolution

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Analysis of Intraspecies Diversity of Rice Reveals Variation Patterns of Oryza sativa Basic Leucine Zippers

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Phyton-International Journal of Experimental Botany 2024年第5期93卷 859-873页

作者： Jing Wang Wenqing Xiao Qingnan Wang Xu Wang Bin Jiang Yangchun Han Yang Sun Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases Key Laboratory for Conservation and Use of Important Biological Resources of Anhui ProvinceCollege of Life SciencesAnhui Normal UniversityWuhu241000China Institute of Plant Protection Jiangsu Academy of Agricultural SciencesNanjing210000China

The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic *** to gene presence/absence variations,it is limited to identify bZIP genes based on the reference ***,we performed the bZIP gene family analysis in the rice *** employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic *** upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during *** analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical ***-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae ***(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different *** Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to *** multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in *** results provide new resources and offer new directions for functional studies of OsbZIPs.

关键词： Rice OsbZIP pan-genome structure variation atypical gene bacterial blight

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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes Marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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Oryza pan-genomics: A new foundation for future rice research and improvement

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The Crop Journal 2021年第3期9卷 622-632页

作者： Chao Huang Zhuo Chen Chengzhi Liang State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice ***-genomics has revolutionized genomic research in ***,rice pan-genomic studies so far have been limited mostly to cultivated accessions,with only a few close wild *** in sequencing technologies have permitted the assembly of highquality rice genome sequences at low cost,making it possible to construct genus-level pan-genomes across all *** this review,we summarize progress in current research on genetic and genomic resources in Oryza,and in sequencing and computational technologies used for rice genome and pangenome *** future work,we discuss the approaches and challenges in the construction of,and data access to,Oryza pan-genomes based on representative high-quality genome *** Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.

关键词： Oryza pan-genome De novo assembly Genetic diversity Wild rice

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The role of genomic structural variation in the genetic improvement of polyploid crops

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The Crop Journal 2019年第2期7卷 127-140页

作者： Sarah-Veronica Schiessl Elvis Katche Elizabeth Ihien Harmeet Singh Chawla Annaliese S.Mason Department of Plant Breeding Justus Liebig University

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

关键词： Presence–absence variation Copy-number variation Homeologous exchanges genome structure pan-genome

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Exploring and Exploiting pan-genomics for Crop Improvement

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Molecular Plant 2019年第2期12卷 156-169页

作者： Yongfu Tao Xianrong Zhao Emma Mace Robert Henry David Jordan Queensland Alliance for Agriculture and Food Innovation (QAAFI) The University of Queensland Hermitage Research Facility Warwick QLD 4370 Australia Agri-Scienee Queensland Department of Agriculture and Fisheries (DAF) Hermitage Research Facility Warwick QLD 4370 Australia Queensland Alliance for Agriculture and Food Innovation (QAAFI) The University of Queensland Brisbane QLD 4072 Australia These authors contributed equally to this article.

Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan?genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.

关键词： pan-genome dispensable genes core genes structural variation crop improvement agronomical traits

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Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

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Genomics, Proteomics & Bioinformatics 2019年第2期17卷 169-182页

作者： Valentina Galata Cédric C. Laczny Christina Backes Georg Hemmrich-Stanisak Susanne Schmolke Andre Franke Eckart Meese Mathias Herrmann Lutz von Müller Achim Plum Rolf Mü ller Cord Stahler Andreas E. Posch Andreas Keller Chair for Clinical Bioinformatics Saarland University 66123 Saarbrücken Germany Helmholtz Center for Infection Research and Pharmaceutical Biotechnology (HZI) Saarland University 66123 Saarbrücken Germany Institute of Clinical Molecular Biology Christian-Albrechts University of Kiel 24105 Kiel Germany Siemens Healthcare GmbH Strategy and Innovation 91052 Erlangen Germany Department of Human Genetics Saarland University 66421 Homburg Germany Institute of Medical Microbiology and Hygiene Saarland University 66421 Homburg Germany Ares Genetics GmbH 1030 Vienna Austria Curetis GmbH 71088 Holzgerlingen Germany Department of Pharmacy Pharmaceutical Biotechnology Saarland University 66123 Saarbrücken Germany Department of Microbial Natural Products Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Saarland University 66123 Saarbrücken Germany

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species,including conserved essential genes and known resis-tance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base,a resource available for academic research use free of charge at https://***.

关键词： Antibiotic resistance Whole-genome sequencing Bacteria pan-genome

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