ArticleGenome biology and evolution2019
Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 45 citations in OpenAlex.
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- Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Insight Into the Nuclear and Mitochondrial Genome of the Caribbean King CrabEcology and evolution · 2025Article
- A draft genome assembly of the reef-building coral Acropora hemprichii from the central Red Sea.Scientific data · 2024Article
- Genomes of the Caribbean reef-building coralsbioRxiv : the preprint server for biology · 2024Article
- Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop.Plant communications · 2024Article
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- Pervasive tandem duplications and convergent evolution shape coral genomes.Genome biology · 2023Article
- Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.Communications biology · 2023Article
- Comparative transcriptome analysis reveals deep molecular landscapes in stony coralFrontiers in genetics · 2023Article
- High-quality genome assembles from key Hawaiian coral species.GigaScience · 2022Article
- Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora.BMC ecology and evolution · 2022Article
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- Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918.Genome biology and evolution · 2021Article
- Molecular mechanisms of sperm motility are conserved in an early-branching metazoan.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The First Draft Genome of a Cold-Water Coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae).Genome biology and evolution · 2021Article
- Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes.Molecular biology and evolution · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, 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 bp, 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.