1
|
Selwyn JD, Vollmer SV. Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis. G3 (BETHESDA, MD.) 2023; 13:jkad232. [PMID: 37804092 PMCID: PMC10700113 DOI: 10.1093/g3journal/jkad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade.
Collapse
Affiliation(s)
- Jason D Selwyn
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Steven V Vollmer
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| |
Collapse
|
2
|
Ying H, Hayward DC, Cooke I, Wang W, Moya A, Siemering KR, Sprungala S, Ball EE, Forêt S, Miller DJ. The Whole-Genome Sequence of the Coral Acropora millepora. Genome Biol Evol 2019; 11:1374-1379. [PMID: 31059562 PMCID: PMC6501875 DOI: 10.1093/gbe/evz077] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - David C Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Weiwen Wang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Kirby R Siemering
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Susanne Sprungala
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Sylvain Forêt
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
3
|
Yang Y, Song X, Tang W. Complete mitochondrial DNA sequence of Pseudogastromyzon changtingensis (Osteichthyes: Gastromyzontidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:871-872. [PMID: 33473661 PMCID: PMC7800118 DOI: 10.1080/23802359.2016.1250135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Pseudogastromyzon changtingensis belonging to the family Gastromyzontidae is a good model for phylogeny and zoogeography research. In the present paper, the sequenced mitochondrial genome of P. changtingensis is of 16573 bp in length, and encodes 13 typical protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The result of phylogenetic analysis demonstrates that P. changtingensis is close to that of P. fasciatus.
Collapse
Affiliation(s)
- Yang Yang
- Laboratory of Ichthyology, Shanghai Ocean University, Shanghai, China.,Shanghai Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China
| | - Xiaojing Song
- Laboratory of Ichthyology, Shanghai Ocean University, Shanghai, China.,Shanghai Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China
| | - Wenqiao Tang
- Laboratory of Ichthyology, Shanghai Ocean University, Shanghai, China.,Shanghai Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China
| |
Collapse
|