دورية أكاديمية
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Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.

التفاصيل البيبلوغرافية
العنوان: Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.
المؤلفون: Young BD; Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA. benjamindouglasyoung1993@gmail.com.; Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA. benjamindouglasyoung1993@gmail.com., Williamson OM; Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA., Kron NS; Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA., Andrade Rodriguez N; Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA., Isma LM; Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA., MacKnight NJ; Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.; Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA., Muller EM; Mote Marine Laboratory, Sarasota, FL, USA., Rosales SM; Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.; Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA., Sirotzke SM; Mote Marine Laboratory, Sarasota, FL, USA., Traylor-Knowles N; Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA., Williams SD; Mote Marine Laboratory, Sarasota, FL, USA., Studivan MS; Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.; Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
المصدر: BMC genomics [BMC Genomics] 2024 Feb 29; Vol. 25 (1), pp. 226. Date of Electronic Publication: 2024 Feb 29.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Transcriptome* , Anthozoa*/genetics, Animals ; Sequence Analysis, DNA/methods ; Genome ; Caribbean Region ; High-Throughput Nucleotide Sequencing/methods
مستخلص: 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.
(© 2024. The Author(s).)
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معلومات مُعتمدة: C2002 Florida Department of Environmental Protection; C2002 Florida Department of Environmental Protection; C2002 Florida Department of Environmental Protection; C2002 Florida Department of Environmental Protection; 1951826 National Science Foundation
فهرسة مساهمة: Keywords: Orbicella faveolata; De-novo genome assembly; HiFi reads; ISO-seq; Long-read sequencing; PacBio circular consensus sequencing; Stony coral Scleractinia
تواريخ الأحداث: Date Created: 20240229 Date Completed: 20240304 Latest Revision: 20240304
رمز التحديث: 20240304
مُعرف محوري في PubMed: PMC10905781
DOI: 10.1186/s12864-024-10092-w
PMID: 38424480
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-024-10092-w