{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:16:36Z","timestamp":1789982196784,"version":"4.0.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T00:00:00Z","timestamp":1561593600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EPS-0903833"],"award-info":[{"award-number":["EPS-0903833"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for Research Excellence in Science and Technology","award":["0833211"],"award-info":[{"award-number":["0833211"]}]},{"name":"Center for Research Excellence in Science and Technology","award":["1345247"],"award-info":[{"award-number":["1345247"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186\u2009kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615\u2009Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700\u2009Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807\u2009bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.<\/jats:p>","DOI":"10.1093\/gbe\/evz135","type":"journal-article","created":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T18:09:16Z","timestamp":1561486156000},"page":"2045-2054","source":"Crossref","is-referenced-by-count":40,"title":["Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1995-9062","authenticated-orcid":false,"given":"Martin","family":"Helmkampf","sequence":"first","affiliation":[{"name":"Tropical Conservation Biology and Environmental Science, University of Hawa\u00edi at Hilo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M Renee","family":"Bellinger","sequence":"additional","affiliation":[{"name":"Tropical Conservation Biology and Environmental Science, University of Hawa\u00edi at Hilo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott M","family":"Geib","sequence":"additional","affiliation":[{"name":"Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Hilo, Hawa\u00edi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheina B","family":"Sim","sequence":"additional","affiliation":[{"name":"Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Hilo, Hawa\u00edi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Misaki","family":"Takabayashi","sequence":"additional","affiliation":[{"name":"Marine Science Department, University of Hawa\u00edi at Hilo"},{"name":"Okinawa Institute of Science and Technology, Onna, Okinawa, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,6,27]]},"reference":[{"issue":"1","key":"2019090906382253300_evz135-B1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s12562-016-1050-4","article-title":"Genome size distribution in phylum Cnidaria","volume":"83","author":"Adachi","year":"2017","journal-title":"Fish Sci"},{"key":"2019090906382253300_evz135-B2","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1101\/gr.88502","article-title":"Automated de novo identification of repeat sequence families in sequenced genomes","volume":"12","author":"Bao","year":"2002","journal-title":"Genome Res"},{"issue":"2","key":"2019090906382253300_evz135-B3","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2019090906382253300_evz135-B4","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.13288","article-title":"Comparative genomics explains the evolutionary success of reef-forming corals","volume":"5","author":"Bhattacharya","year":"2016","journal-title":"eLife"},{"issue":"8","key":"2019090906382253300_evz135-B5","doi-asserted-by":"crossref","first-page":"e72466.","DOI":"10.1371\/journal.pone.0072466","article-title":"Does coral disease affect symbiodinium? 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