{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:17Z","timestamp":1772138057321,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T00:00:00Z","timestamp":1668124800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole-genome resequencing data. We demonstrate CAPG in allotetraploids, where it performs better than Genome Analysis Toolkit\u2019s HaplotypeCaller applied to reads aligned to the combined subgenomic references.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Code and tutorials are available at https:\/\/github.com\/Kkulkarni1\/CAPG.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac729","type":"journal-article","created":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T07:19:06Z","timestamp":1668151146000},"source":"Crossref","is-referenced-by-count":5,"title":["CAPG: comprehensive allopolyploid genotyper"],"prefix":"10.1093","volume":"39","author":[{"given":"Roshan","family":"Kulkarni","sequence":"first","affiliation":[{"name":"Department of Agronomy, Iowa State University , Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yudi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Iowa State University , Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven B","family":"Cannon","sequence":"additional","affiliation":[{"name":"USDA\u2014Agricultural Research Service, Corn Insects and Crop Genetics Research Unit , Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3650-0018","authenticated-orcid":false,"given":"Karin S","family":"Dorman","sequence":"additional","affiliation":[{"name":"Department of Statistics, Iowa State University , Ames, IA 50011, USA"},{"name":"Department of Genetics, Development and Cell Biology, Iowa State University , Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,11,11]]},"reference":[{"key":"2023010805382309900_btac729-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023010805382309900_btac729-B2","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/ng.3517","article-title":"The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut","volume":"48","author":"Bertioli","year":"2016","journal-title":"Nat. Genet"},{"key":"2023010805382309900_btac729-B3","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/s41588-019-0405-z","article-title":"The genome sequence of segmental allotetraploid peanut Arachis hypogaea","volume":"51","author":"Bertioli","year":"2019","journal-title":"Nat. Genet"},{"key":"2023010805382309900_btac729-B4","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1093\/bioinformatics\/btx587","article-title":"SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data","volume":"34","author":"Blischak","year":"2018","journal-title":"Bioinformatics"},{"key":"2023010805382309900_btac729-B5","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1534\/g3.118.200913","article-title":"polyRAD: genotype calling with uncertainty from sequencing data in polyploids and diploids","volume":"9","author":"Clark","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"2023010805382309900_btac729-B6","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.molp.2015.02.002","article-title":"Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations","volume":"8","author":"Clevenger","year":"2015","journal-title":"Mol. Plant"},{"key":"2023010805382309900_btac729-B7","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.molp.2016.11.015","article-title":"Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut","volume":"10","author":"Clevenger","year":"2017","journal-title":"Mol. Plant"},{"key":"2023010805382309900_btac729-B8","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1534\/g3.115.019703","article-title":"SWEEP: a tool for filtering high-quality SNPs in polyploid crops","volume":"5","author":"Clevenger","year":"2015","journal-title":"G3 (Bethesda)"},{"key":"2023010805382309900_btac729-B9","doi-asserted-by":"crossref","first-page":"564","DOI":"10.3389\/fpls.2018.00564","article-title":"Haplotype-based genotyping in polyploids","volume":"9","author":"Clevenger","year":"2018","journal-title":"Front. Plant Sci"},{"key":"2023010805382309900_btac729-B10","first-page":"241","volume-title":"Peanuts Genetics, Processing, and Utilization","author":"Dash","year":"2016"},{"key":"2023010805382309900_btac729-B11","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41588-018-0116-x","article-title":"Resequencing of 243 diploid cotton accessions based on an updated a genome identifies the genetic basis of key agronomic traits","volume":"50","author":"Du","year":"2018","journal-title":"Nat. Genet"},{"key":"2023010805382309900_btac729-B12","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II. Error probabilities","volume":"8","author":"Ewing","year":"1998","journal-title":"Genome Res"},{"key":"2023010805382309900_btac729-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-017-1167-5","article-title":"Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons","volume":"18","author":"Fang","year":"2017","journal-title":"Genome Biol"},{"key":"2023010805382309900_btac729-B14","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1534\/genetics.118.301468","article-title":"Genotyping polyploids from messy sequencing data","volume":"210","author":"Gerard","year":"2018","journal-title":"Genetics"},{"key":"2023010805382309900_btac729-B15","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.3390\/genes11101220","article-title":"Use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes","volume":"11","author":"Kulkarni","year":"2020","journal-title":"Genes"},{"key":"2023010805382309900_btac729-B16","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nbt.3208","article-title":"Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution","volume":"33","author":"Li","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023010805382309900_btac729-B17","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2023010805382309900_btac729-B18","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023010805382309900_btac729-B19","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1111\/mec.13601","article-title":"Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing","volume":"25","author":"Limborg","year":"2016","journal-title":"Mol. Ecol"},{"key":"2023010805382309900_btac729-B20","first-page":"1","article-title":"Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement","volume":"10","author":"Lu","year":"2019","journal-title":"Nat. Commun"},{"key":"2023010805382309900_btac729-B21","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/978-1-4939-1966-6_12","volume-title":"Plant Genotyping: Methods and Protocols, Methods in Molecular Biology","author":"Mason","year":"2015"},{"key":"2023010805382309900_btac729-B22","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2023010805382309900_btac729-B23","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nrg2986","article-title":"Genotype and SNP calling from next-generation sequencing data","volume":"12","author":"Nielsen","year":"2011","journal-title":"Nat. Rev. Genet"},{"key":"2023010805382309900_btac729-B24","doi-asserted-by":"crossref","first-page":"560096","DOI":"10.3389\/fpls.2020.560096","article-title":"Sequencing multiple cotton genomes reveals complex structures and lays foundation for breeding","volume":"11","author":"Pan","year":"2020","journal-title":"Front. Plant Sci"},{"key":"2023010805382309900_btac729-B25","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/j.1469-8137.2009.03142.x","article-title":"Evolutionary consequences of autopolyploidy","volume":"186","author":"Parisod","year":"2010","journal-title":"New Phytol"},{"key":"2023010805382309900_btac729-B26","doi-asserted-by":"crossref","first-page":"5151","DOI":"10.1093\/bioinformatics\/btaa648","article-title":"AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data","volume":"36","author":"Peng","year":"2021","journal-title":"Bioinformatics"},{"key":"2023010805382309900_btac729-B27","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1007\/s00438-017-1327-z","article-title":"Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences","volume":"292","author":"Peng","year":"2017","journal-title":"Mol. Genet. Genomics"},{"key":"2023010805382309900_btac729-B28","doi-asserted-by":"crossref","first-page":"222","DOI":"10.3389\/fgene.2020.00222","article-title":"Comparison of SNP calling pipelines and NGS platforms to predict the genomic regions harboring candidate genes for nodulation in cultivated peanut","volume":"11","author":"Peng","year":"2020","journal-title":"Front. Genet"},{"key":"2023010805382309900_btac729-B29","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/msb.2011.54","article-title":"AlleleSeq: analysis of allele-specific expression and binding in a network framework","volume":"7","author":"Rozowsky","year":"2011","journal-title":"Mol. Syst. Biol"},{"key":"2023010805382309900_btac729-B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3835\/plantgenome2016.06.0052","article-title":"Target amplicon sequencing for genotyping genome-wide single nucleotide polymorphisms identified by whole-genome resequencing in peanut","volume":"9","author":"Shirasawa","year":"2016","journal-title":"The Plant Genome"},{"key":"2023010805382309900_btac729-B31","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-31442-1","volume-title":"Polyploidy and Genome Evolution","author":"Soltis","year":"2012"},{"key":"2023010805382309900_btac729-B32","first-page":"314","author":"Vasimuddin","year":"2019"},{"key":"2023010805382309900_btac729-B33","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1038\/s41588-018-0282-x","article-title":"Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense","volume":"51","author":"Wang","year":"2019","journal-title":"Nat. Genet"},{"key":"2023010805382309900_btac729-B34","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.3732\/ajb.1500320","article-title":"The wondrous cycles of polyploidy in plants","volume":"102","author":"Wendel","year":"2015","journal-title":"Am. J. Bot"},{"key":"2023010805382309900_btac729-B35","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1186\/1471-2164-15-351","article-title":"Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq)","volume":"15","author":"Zhou","year":"2014","journal-title":"BMC Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac729\/48000507\/btac729.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac729\/48521014\/btac729.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac729\/48521014\/btac729.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T00:39:21Z","timestamp":1673138361000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac729\/6823535"}},"subtitle":[],"editor":[{"given":"Karsten","family":"Borgwardt","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,11]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac729","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.04.21.488948","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,11,11]]},"article-number":"btac729"}}