{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T09:49:37Z","timestamp":1777974577800,"version":"3.51.4"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,1,12]],"date-time":"2021-01-12T00:00:00Z","timestamp":1610409600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31661143013"],"award-info":[{"award-number":["31661143013"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31790414"],"award-info":[{"award-number":["31790414"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jinxinnong Animal Science Development Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations\u20149 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.<\/jats:p>","DOI":"10.1093\/bib\/bbaa399","type":"journal-article","created":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T21:38:17Z","timestamp":1607463497000},"source":"Crossref","is-referenced-by-count":5,"title":["Integrated hybrid <i>de novo<\/i> assembly technologies to obtain high-quality pig genome using short and long reads"],"prefix":"10.1093","volume":"22","author":[{"given":"Heng","family":"Du","sequence":"first","affiliation":[{"name":"National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenguang","family":"Diao","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengju","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5766-7864","authenticated-orcid":false,"given":"Jian-Feng","family":"Liu","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,12]]},"reference":[{"issue":"7","key":"2021090907255577100_ref1","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1146\/annurev-animal-020518-115344","article-title":"New approaches for genome assembly and scaffolding","volume":"4","author":"Rice","year":"2019","journal-title":"Annu Rev Anim Biosci"},{"key":"2021090907255577100_ref2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1038\/nmeth1156","article-title":"Next-generation sequencing transforms today\u2019s biology","volume":"5","author":"Schuster","year":"2008","journal-title":"Nat Methods"},{"key":"2021090907255577100_ref3","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature03001","article-title":"Finishing the euchromatic sequence of the human genome","volume":"431","author":"International Human Genome Sequencing Consortium","year":"2004","journal-title":"Nature"},{"key":"2021090907255577100_ref4","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/s41576-018-0003-4","article-title":"Piercing the dark matter: bioinformatics of long-range sequencing and mapping","volume":"19","author":"Sedlazeck","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2021090907255577100_ref5","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ygeno.2017.01.005","article-title":"Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis","volume":"109","author":"Guo","year":"2017","journal-title":"Genomics"},{"key":"2021090907255577100_ref6","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/nature01019","article-title":"Evolution, consequences and future of plant and animal domestication","volume":"418","author":"Diamond","year":"2002","journal-title":"Nature"},{"issue":"2","key":"2021090907255577100_ref7","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1146\/annurev-animal-022513-114129","article-title":"Domestication genomics: evidence from animals","volume":"4","author":"Wang","year":"2014","journal-title":"Annual Review of Animal Biosciences"},{"issue":"Suppl 1","key":"2021090907255577100_ref8","doi-asserted-by":"crossref","first-page":"9971","DOI":"10.1073\/pnas.0901586106","article-title":"From wild animals to domestic pets, an evolutionary view of domestication","volume":"106","author":"Driscoll","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2021090907255577100_ref9","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.tig.2013.01.003","article-title":"Burger JJTiG. 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