Gigabyte, Journal Year: 2023, Volume and Issue: 2023, P. 1 - 12
Published: March 16, 2023
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from southeastern coast USA, first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data an initial proximity ligation scaffolding. The was annotated using evidence transcripts, proteins, ab initio gene model predictions. This is comparable high-quality reference genomes corals. comprises 2,858 scaffolds (N50 1.6 Mbp) has size 556.9 Mbp. Approximately 57% repetitive elements 34% coding DNA. predicted 41,089 genes, including 91.1% complete metazoan orthologs. will facilitate investigations into ecology this species evolution
Language: Английский
Citations
5
BMC Research Notes, Journal Year: 2024, Volume and Issue: 17(1)
Published: Oct. 29, 2024
Abstract Objective The connectivity and genetic structuring of populations throughout a region influence species’ resilience probability recovery from anthropogenic impacts. By gaining comprehensive understanding population connectivity, more effective management can be prioritized. To assess the structure common cold-water coral species, Desmophyllum pertusum ( Lophelia pertusa ), we performed Restriction-site Associated DNA Sequencing (RADseq) on individuals nine sites ranging submarine canyons off New England to southeastern coast United States (SEUS) Gulf Mexico (GOM). Fifty-seven 3,180 single-nucleotide polymorphisms (SNPs) were used differentiation. Results High exists among along SEUS, yet these differentiated those north in Norfolk Canyon North Atlantic States, as well GOM. Interestingly, Canyon, located just Carolina, GOM exhibited low levels differentiation, corroborating previous microsatellite analyses signifying gene flow between populations. Increasing sample sizes existing including additional sampling over larger geographic range would help define potential source reveal fine-scale patterns D.
Language: Английский
Citations
1
Coral reefs of the world, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 30
Published: Jan. 1, 2023
Language: Английский
Citations
2
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 22, 2024
Corals populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, critically endangered coral species compared reefs the larger Indo-Pacific. reef corals also long diverged from their Pacific counterparts may have evolved different survival strategies. Most genomic resources been developed for which impede our ability study changes in genetic composition communities response global change. To help fill gap resources, we used PacBio HiFi sequencing generate first genome assemblies three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, Siderastrea siderea. We explore novelties that shape scleractinian genomes. Notably, find abundant gene duplications all classes (e.g., tandem segmental), especially S. This has one largest genomes any (822Mb) seems be driven by repetitive content family expansion diversification. As size siderea was double expected stony evaluated possibility an ancient whole duplication using Ks tests found no evidence such event species. By presenting these assemblies, hope develop better understanding evolution as enable researchers further investigate population genetics diversity
Language: Английский
Citations
0
Published: Oct. 18, 2023
Citations
0