A Reference Genome Assembly of the Bobcat, Lynx rufus

et al. 2022

Self Cite

Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.

Section: Methodsmentioning

confidence: 99%

Reference Genome of the Black Surfperch,Embiotoca jacksoni(Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage

Bernardi

Toy

et al. 2022

Self Cite

“…We assembled the nuclear genome of M. californianus following the CCGP assembly protocol Version 3.0 ( Table 1 , Lin et al 2022 ). We assembled the mitochondrial genome from the PacBio HiFi reads using the reference-guided pipeline MitoHiFi ( https://github.com/marcelauliano/MitoHiFi ) ( Allio et al 2020 ) and the Mytilus trossulus mitochondrial genome (NCBI:GU936626.1) as the starting reference sequence.…”

Section: Methodsmentioning

confidence: 99%

“…We assembled the mitochondrial genome from the PacBio HiFi reads using the reference-guided pipeline MitoHiFi ( https://github.com/marcelauliano/MitoHiFi ) ( Allio et al 2020 ) and the Mytilus trossulus mitochondrial genome (NCBI:GU936626.1) as the starting reference sequence. Full assembly details are available in Lin et al (2022) .…”

Section: Methodsmentioning

confidence: 99%

“…We estimated genome size, heterozygosity, repeat content, sequencing error, and genome assembly completeness following standard protocols established by the CCGP and described in detail by Lin et al (2022) . We assessed assembly quality of the M. californianus primary and alternate genomes using BUSCO ( Simão et al 2015 ; Seppey et al 2019 ) with the Mollusca ortholog database (mollusca_odb10) which contains 5,295 genes.…”

Section: Methodsmentioning

confidence: 99%

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Reference genome for the California ribbed mussel,Mytilus californianus, an ecosystem engineer

Paggeot

DeBiasse

et al. 2022

The California ribbed mussel, Mytilus californianus, is an ecosystem engineer crucial for the survival of many marine species inhabiting the intertidal zone of California. Here, we describe the first reference genome for M. californianus and compare it to previously published genomes from three other Mytilus species: M. edulis, M. coruscus, and M. galloprovincialis. The M. californianus reference genome is 1.65 Gb in length, with N50 sequence length of 118Mb, and an estimated 86.0% complete single copy genes. Compared to the other three Mytilus species, the M. californianus genome assembly is the longest, has the highest N50 value, and the highest percentage complete single copy genes. This high-quality genome assembly provides a foundation for population genetic analyses that will give insight into future conservation work along the coast of California.

“…We assembled the genome of the giant pink sea star following the California Conservation Genomics Project (CCGP) assembly protocol Version 4.0, introduced in ( Lin et al 2022 ). The difference between versions relies on the output sequences from HiFiasm [Version 0.16.1-r375] ( Cheng et al 2021 ) that are used to generate the final assembly (see Table 1 for assembly pipeline and relevant software).…”

Section: Methodsmentioning

confidence: 99%

A chromosome-level reference genome for the giant pink sea star,Pisaster brevispinus, a species severely impacted by wasting

DeBiasse

Schiebelhut

et al. 2022

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads, and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6Mb and a scaffold N50 of 21.4Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the sister species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.