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J Hered
2022 Nov 30;1136:649-656. doi: 10.1093/jhered/esac032.
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Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems.
Bernardi G
,
DeBiasse M
,
Escalona M
,
Marimuthu MPA
,
Nguyen O
,
Sacco S
,
Beraut E
,
Miller C
,
Toffelmier E
,
Shaffer HB
.
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Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales, sea otter, sea urchin, kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the California Sheephead, Semicossyphus pulcher. We present a reference genome for this ecologically important species that will serve as a key resource for future conservation research of California's inshore marine environment utilizing genomic tools to address changes in life-history traits, dispersal, range shifts, and ecological interactions among members of the kelp forest ecological assemblages. Our genome assembly of S. pulcher has a total length of 0.794 Gb, which is similar to many other marine fishes. The assembly is largely contiguous (N50 = 31.9 Mb) and nearly complete (BUSCO single-copy core gene content = 98.1%). Within the context of the California Conservation Genomics Project (CCGP), the genome of S. pulcher will be used as an important reference resource for ongoing whole genome resequencing efforts of the species.
Abdennur,
Cooler: scalable storage for Hi-C data and other genomically labeled arrays.
2020, Pubmed
Abdennur,
Cooler: scalable storage for Hi-C data and other genomically labeled arrays.
2020,
Pubmed
Almeida,
Chromosomal Evolution and Cytotaxonomy in Wrasses (Perciformes; Labridae).
2017,
Pubmed
Beldade,
Historical biogeography and speciation in the Creole wrasses (Labridae, Clepticus).
2009,
Pubmed
Bernardi,
Vicariance and dispersal across Baja California in disjunct marine fish populations.
2003,
Pubmed
Bucciarelli,
An ultracentrifugation analysis of two hundred fish genomes.
2002,
Pubmed
Burt,
Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts.
2018,
Pubmed
,
Echinobase
Camacho,
BLAST+: architecture and applications.
2009,
Pubmed
Challis,
BlobToolKit - Interactive Quality Assessment of Genome Assemblies.
2020,
Pubmed
Cheng,
Haplotype-resolved assembly of diploid genomes without parental data.
2022,
Pubmed
Ghurye,
Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
2019,
Pubmed
Guan,
Identifying and removing haplotypic duplication in primary genome assemblies.
2020,
Pubmed
Gurevich,
QUAST: quality assessment tool for genome assemblies.
2013,
Pubmed
Hamilton,
Size-selective harvesting alters life histories of a temperate sex-changing fish.
2007,
Pubmed
Kerpedjiev,
HiGlass: web-based visual exploration and analysis of genome interaction maps.
2018,
Pubmed
Korlach,
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.
2017,
Pubmed
Molina,
Karyoevolutionary aspects of Atlantic hogfishes (Labridae-Bodianinae), with evidence of an atypical decondensed argentophilic heterochromatin.
2012,
Pubmed
Oliver,
Longer and more frequent marine heatwaves over the past century.
2018,
Pubmed
Poortvliet,
Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality.
2013,
Pubmed
Ramírez,
High-resolution TADs reveal DNA sequences underlying genome organization in flies.
2018,
Pubmed
Ranallo-Benavidez,
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
2020,
Pubmed
Rhie,
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
2020,
Pubmed
Sanford,
Widespread shifts in the coastal biota of northern California during the 2014-2016 marine heatwaves.
2019,
Pubmed
Shaffer,
Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project.
2022,
Pubmed
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Smith,
Behavioral responses across a mosaic of ecosystem states restructure a sea otter-urchin trophic cascade.
2021,
Pubmed
,
Echinobase
Westneat,
Phylogenetic relationships and evolutionary history of the reef fish family Labridae.
2005,
Pubmed
Yukai,
The complete mitochondrial genome of Thalassoma lunare (Labriformes, Labridae).
2019,
Pubmed
