Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing
Abstract Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10092-w |
| _version_ | 1797275769657884672 |
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| author | Benjamin D. Young Olivia M. Williamson Nicholas S. Kron Natalia Andrade Rodriguez Lys M. Isma Nicholas J. MacKnight Erinn M. Muller Stephanie M. Rosales Stephanie M. Sirotzke Nikki Traylor-Knowles Sara D. Williams Michael S. Studivan |
| author_facet | Benjamin D. Young Olivia M. Williamson Nicholas S. Kron Natalia Andrade Rodriguez Lys M. Isma Nicholas J. MacKnight Erinn M. Muller Stephanie M. Rosales Stephanie M. Sirotzke Nikki Traylor-Knowles Sara D. Williams Michael S. Studivan |
| author_sort | Benjamin D. Young |
| collection | DOAJ |
| description | Abstract Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of ‘omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other ‘omics analyses to aid in the conservation of this species. |
| first_indexed | 2024-03-07T15:19:11Z |
| format | Article |
| id | doaj.art-a01e8cb9048b4f3fade0a09b4de212cf |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:19:11Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-a01e8cb9048b4f3fade0a09b4de212cf2024-03-05T17:46:57ZengBMCBMC Genomics1471-21642024-02-0125111210.1186/s12864-024-10092-wAnnotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencingBenjamin D. Young0Olivia M. Williamson1Nicholas S. Kron2Natalia Andrade Rodriguez3Lys M. Isma4Nicholas J. MacKnight5Erinn M. Muller6Stephanie M. Rosales7Stephanie M. Sirotzke8Nikki Traylor-Knowles9Sara D. Williams10Michael S. Studivan11Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiDepartment of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiDepartment of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiDepartment of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiDepartment of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiCooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiMote Marine LaboratoryCooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiMote Marine LaboratoryDepartment of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiMote Marine LaboratoryCooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of MiamiAbstract Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of ‘omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other ‘omics analyses to aid in the conservation of this species.https://doi.org/10.1186/s12864-024-10092-wDe-novo genome assemblyOrbicella faveolataPacBio circular consensus sequencingHiFi readsLong-read sequencingISO-seq |
| spellingShingle | Benjamin D. Young Olivia M. Williamson Nicholas S. Kron Natalia Andrade Rodriguez Lys M. Isma Nicholas J. MacKnight Erinn M. Muller Stephanie M. Rosales Stephanie M. Sirotzke Nikki Traylor-Knowles Sara D. Williams Michael S. Studivan Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing BMC Genomics De-novo genome assembly Orbicella faveolata PacBio circular consensus sequencing HiFi reads Long-read sequencing ISO-seq |
| title | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing |
| title_full | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing |
| title_fullStr | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing |
| title_full_unstemmed | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing |
| title_short | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing |
| title_sort | annotated genome and transcriptome of the endangered caribbean mountainous star coral orbicella faveolata using pacbio long read sequencing |
| topic | De-novo genome assembly Orbicella faveolata PacBio circular consensus sequencing HiFi reads Long-read sequencing ISO-seq |
| url | https://doi.org/10.1186/s12864-024-10092-w |
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