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. 2022 Nov 30;113(6):681–688. doi: 10.1093/jhered/esac041

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

Lisa X Paggeot 1,✉, Melissa B DeBiasse 2, Merly Escalona 3, Colin Fairbairn 4, Mohan P A Marimuthu 5, Oanh Nguyen 6, Ruta Sahasrabudhe 7, Michael N Dawson 8
Editor: Rachel Meyer
PMCID: PMC9710001  PMID: 35947871

Abstract

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 118 Mb, and an estimated 86.0% complete single copy genes. Compared with 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.

Keywords: Bivalvia, California Conservation Genomics Project (CCGP), ecosystem engineer, marine invertebrate, mussel, rocky intertidal

Introduction

Ecosystem engineers modify the physical environment in a way that changes available habitats (Jones et al. 1994). Their modifications can lead to alteration, expansion, or formation of novel habitats and promote the success of taxa in their vicinity (Dayton 1972; Bruno et al. 2003). The California ribbed mussel, Mytilus californianus, an intertidal species distributed along the west coast of North America from the Aleutian Islands to Isla Socorro, Mexico (Fig. 1A; Soot-Ryen 1955), is an ecosystem engineer known for its role in the origin of the Keystone Species concept (Fig. 1B; Paine 1966). Ribbed mussels form large compact beds, attached to underlying rock, that generate many protected interstices inhabited by other organisms (Paine 1994; Gutiérrez et al. 2003). The mussel-rock attachment is by byssal threads (Waite 2017), a feature that is widespread among marine bivalves though stronger in M. californianus than in its congeners (Holten-Andersen et al. 2009) and different in mytilids versus other bivalves (Pearce and Labarbera 2009).

Fig. 1.

Fig. 1.

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The distribution of the California ribbed mussel, Mytilus californianus. (A) World map (inset) and continental map showing the reported geographic range of M. californianus, from the Aleutian Islands to Isla Socorro, Mexico (Soot-Ryen 1955). Other authors have since reported a narrower distribution, such as from Baja California to British Columbia (Sagarin and Somero 2006). Yellow star indicates the geographic location of the sample collected and used to generate the genome. (B) A bed of M. californianus mussels at Duxbury Reef, Marin County, CA. Note the other species that inhabit the ribbed mussel beds such as the acorn and stalked barnacle. Globe image in panel A taken from https://www.clipsafari.com/clips/o29983-globe-showing-north-america. Panel B photo credit: Michael N Dawson.

In addition to its role in important ecological functions, Mytilus has been a rich model system for breaking new ground in the field of marine genetics. For example, analyses of two polymorphic loci (Lap and Pgi) led Tracey et al. (1975) to suggest that homozygote excess is more apparent in juveniles than in adults due to breeding subpopulation structure within the reproductive population. Analyses of hybrid zones where distributions of Mytilus species overlap across the Atlantic and Pacific oceans advanced understanding of evolutionary processes in high dispersal species (Riginos and Cunningham 2004, Springer and Crespi 2006). And, exploiting the biparental inheritance of mtDNA in mussels, Śmietanka et al. (2010) sequenced both mitochondrial genomes of M. trossulus to identify that the mitogenome, which often has been treated as neutral in phylogeographic studies, likely contains multiple adaptive mutations. However, many of these previous genetic studies in Mytilus relied on a small number of loci, therefore limiting inference to small portions of the genome. Extending the genomic resources available would help us better understand the breadth of genomic evolution and its consequences in ecological contexts. Such genomic resources also will illuminate the genetic architecture underlying traits related to physiological tolerance and mechanisms of reproductive compatibility as well as adaptive potential of populations and species in the face of global change (Place et al. 2008; Savolainen et al. 2013; Kinoshita and Seki 2014).

Here, we present a reference genome for M. californianus and compare it with the previously published genomes of three other Mytilus species whose ranges cover the Mediterranean Sea (M. galloprovincialis), the coasts of China, Korea, Japan (Mytilus coruscus), and the western Pacific Ocean (Mytilus edulis). The M. californianus reference genome will contribute to conservation and management of regional biodiversity in California (Shaffer et al. 2022) and has the potential to provide new insights into responses to anthropogenic events and help identify consequences of local and/or regional genetic variation. In addition, the M. californianus reference genome will give us a better understanding of comparative genomics across multiple Mytilus species living around the globe.

Methods

Biological materials

One California mussel was collected from McClures Beach, Marin County, CA, USA (38.1813, −122.9644) on July 22, 2020 by Michael N Dawson. The specimen was transported live to the University of California, Davis, where subsamples of dissected tissue were flash frozen in liquid nitrogen. A voucher specimen (M0D057914Y) is archived in the Dawson Lab collection at University of California, Merced.

Nucleic acid extraction, library prep, and sequencing

We extracted DNA and prepped libraries following standard methods established for marine invertebrates by the California Conservation Genomics Project (CCGP) as described in DeBiasse et al. (2022) and available in Supplementary Information. In brief, we extracted high-molecular-weight (HMW) DNA from 40 mg of the mantle tissue using the Nanobind Tissue Big DNA kit (Pacific BioSciences [PacBio], CA) with the following minor modifications: we performed an additional wash with the CT buffer for the tissue homogenate and pelleted it by centrifuging at 18,000 × g (4 °C for 5 min) to remove any residual buffer before proceeding with the lysis step. We prepared the HiFi SMRTbell library using the SMRTbell Express Template Prep Kit v2.0 (PacBio) and sequenced the 15 to 20 kb average HiFi SMRTbell library using three SMRT Cell 8M Trays. We prepared the Omni-C library using the Dovetail Omni-C Kit (Dovetail Genomics, CA) according to the manufacturer’s protocol with the following modifications: we optimized the digest with 2 µL of Nuclease Enzyme Mix input and the proximity ligation reaction with 500 ng DNA input. We sequenced the library at the Vincent J. Coates Genomics Sequencing Laboratory at University of California, Berkeley (Berkeley, CA) on an Illumina NovaSeq platform (Illumina, CA) targeting approximately 100 million 150 bp paired end reads per gigabase of genome size.

Nuclear and mitochondrial genome assembly

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. Full assembly details are available in Lin et al. (2022).

Table 1.

Assembly pipeline and software usage.

Assembly Software and optionsa Version
Filtering PacBio HiFi adapters HiFiAdapterFilt Commit 64d1c7b
k-mer counting Meryl (k = 21) 1
Estimation of genome size and heterozygosity GenomeScope 2
De novo assembly (contiging) HiFiasm (HiC mode, --primary, p_ctg, and a_ctg output) 0.16.1-r375
Remove low-coverage, duplicated contigs purge_dups 1.2.6
Scaffolding
 Omni-C scaffolding SALSA (-DNASE, -i 20, -p yes) 2
 Gap closing YAGCloser (-mins 2 -f 20 -mcc 2 -prt 0.25 -eft 0.2 -pld 0.2) Commit
20e2769
Omni-C Contact map generation
 Short-read alignment BWA-MEM (-5SP) 0.7.17-r1188
 SAM/BAM processing Samtools 1.11
 SAM/BAM filtering Pairtools 0.3.0
 Pairs indexing Pairix 0.3.7
 Matrix generation Cooler 0.8.10
 Matrix balancing hicExplorer (hicCorrectmatrix correct --filterThreshold -2 4) 3.6
 Contact map visualization HiGlass 2.1.11
PretextMap 0.1.4
PretextView 0.1.5
PretextSnapshot 0.0.3
Organelle assembly
 Mitogenome assembly MitoHiFi (-r , -p 50, -o 1) 2 Commit
c06ed3e
Genome quality assessment
 Basic assembly metrics QUAST (--est-ref-size) 5.0.2
 Assembly completeness BUSCO (-m geno, -l mollusca) 5.0.0
Merqury 1
Contamination screening
 Local alignment tool BLAST+ 2.10
 General contamination screening BlobToolKit 2.3.3
Comparison analysis
 Assembly completeness BUSCO (https://gvolante.riken.jp/) 5.0.0
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Software citations are listed in the text (Rhie et al. 2020).

Options detailed for nondefault runs.

Genome size estimation and quality assessment

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. Following data availability and quality metrics established by Rhie et al. (2021), we used the derived genome quality notation x·y·Q, where x = log10[contig NG50]; y = log10[scaffold NG50]; Q = Phred base accuracy QV (quality value); C = % genome represented by the first “n” scaffolds, following a known karyotype of 2n = 28 (Ahmed and Sparks 1970). Quality metrics for the notation were calculated on the primary assembly.

Under the assumption that the longest scaffolds contain the majority of the genome sequence and represent the putative chromosomes, we generated a histogram of scaffold lengths for 1) the largest 20 scaffolds and 2) all scaffolds and then performed a k-means clustering in R (R Core Team 2020) to test if a drop-off in scaffold size corresponded to the number of chromosomes predicted for Mytilus mussels, including M. californianus (Ahmed and Sparks 1970, Pérez-García et al. 2014).

Comparison to previously published Mytilus genomes

We downloaded the complete genome sequences for the mussels M. edulis (GCA_019925275.1), M. galloprovincialis (GCA_900618805.1), and M. coruscus (GCA_017311375.1) from GenBank. We calculated common metrics of assembly completeness across the three published Mytilus genomes and the M. californianus genome generated here using BUSCO [Version 5.0.0] and the Mollusca ortholog database (mollusca_odb10) as implemented in gVolante (Nishimura et al. 2019).

Results

Nucleic acid extraction, library prep, and sequencing

Extracted HMW DNA had purity 260/280 = 1.83 and 260/230 = 1.91, concentration 169 ng/µl (19.4 µg total), and good integrity with >84% of DNA fragments being 120 kb or more. Sequencing resulted in 5.1 million PacBio HiFi reads representing ~45-fold coverage (N50 read length 14,054 bp; minimum read length 45 bp; mean read length 13,449 bp; maximum read length of 50,337 bp) based on the Genomescope2.0 genome size estimation of 1.576 Gb. Based on PacBio HiFi reads, we estimated 0.09% sequencing error rate and 2.73% nucleotide heterozygosity rate. The Illumina sequencing yielded 203.3 million 150 bp paired end Omni-C reads.

Nuclear and mitochondrial genome assembly

We generated a de novo nuclear genome assembly of the California mussel (xbMytCali1) for which assembly statistics are reported in Table 2 and Fig. 2B. The k-mer spectrum output shows a bimodal distribution with two major peaks, at ~21 and ~42-fold coverage, where peaks correspond to homozygous and heterozygous states respectively of a diploid species. The Omni-C contact map suggests that the primary assembly is highly contiguous (Fig. 2C). The alternate assembly, which consists of sequence from heterozygous regions, is less contiguous (Supplementary Fig. S1). We have deposited both the primary and alternate scaffolds to NCBI.

Table 2.

Sequencing and assembly statistics, and accession numbers.

Bio Projects & Vouchers CCGP NCBI BioProject PRJNA720569
Genera NCBI BioProject PRJNA765636
Species NCBI BioProject PRJNA777198
NCBI BioSample SAMN24505264
Specimen identification M0D057914Y
NCBI Genome accessions Primary Alternate
Assembly accession GCA_021869535.1 GCA_021869935.1
Genome sequences JAKFGE000000000 JAKFGF000000000
Genome sequence PacBio HiFi reads Run 3 PACBIO_SMRT (Sequel II), 5.8 M spots, 81.4 G bases, 48.5 Gb
Accession SRR18000156
Omni-C Illumina reads Run 2 Illumina HiSeq X Ten runs: 203.3 M spots, 61.4 G bases, 20.3 Gb
Accession SRR18000154-55
Genome Assembly Quality Metrics Assembly identifier (quality codea) xbMytCali1 (7.7.Q60.C86)
HiFi read coverageb 45.05X
Primary Alternate
Number of contigs 498 38,455
Contig N50 (bp) 16,323,199 167,345
Contig NG50 (bp) 17,177,226 251,220
Longest contigs (bp) 57,759,394 3,992,896
Number of scaffolds 176 38,315
Scaffold N50 (bp) 117,871,512 169,002
Scaffold NG50 (bp) 120,330,192 253,008
Largest scaffold (bp) 142,435,203 3,992,896
Size of final assembly (bp) 1,651,966,901 2,213,012,655
Gaps per Gbp (#Gaps) 37 (324) 63 (140)
Indel QV (frame shift) 51.43139759 51.43139759
Base pair QV 65.0891 58.9335
Full assembly = 60.6658
k-mer completeness 67.2429 68.2222
Full assembly = 92.3895
BUSCO completeness (mollusca), n = 5,295 C S D F M
Pc 86.00% 85.10% 0.90% 3.30% 10.70%
Ac 85.20% 80.00% 5.20% 4.50% 10.30%
Organelles 1 Complete mitochondrial sequence CM038905.1
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Assembly quality code x·y·Q·C derived notation, from (Rhie et al. 2021). x = log10[contig NG50]; y = log10[scaffold NG50]; Q = Phred base accuracy QV (quality value); C = % genome represented by the first “n” scaffolds, following a known karyotype of 2n = 28. Quality code for all the assembly denoted by primary assembly (xbMytCali1.0.p). BUSCO scores. (C)omplete and (S)ingle; (C)omplete and (D)uplicated; (F)ragmented and (M)issing BUSCO genes. n, number of BUSCO genes in the set/database.

Read coverage and NGx statistics have been calculated based on the estimated genome size of 1.576 Gb.

(P)rimary and (A)lternate assembly values.

Fig. 2.

Fig. 2.

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Visual overview of genome assembly metrics. (A) k-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome. k-mers covered at lower coverage but higher frequency correspond to differences between haplotypes, whereas the higher coverage but lower frequency k-mers correspond to the similarities between haplotypes. The pattern observed corresponds to a k-mer profile for a highly heterozygous species. (B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Mytilus californianus primary assembly (xbMytCali1). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly. The dark vs. light blue area around it shows mean, maximum and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020). (C) Omni-C contact maps for the primary genome assembly generated with PretextSnapshot. Omni-C contact maps translate proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two such regions. Scaffolds are separated by black lines, wherein higher density of black lines corresponds to higher levels of fragmentation. (D) Histogram of the 20 longest scaffold reads for Mytilus californianus. Scaffold size is given in megabase pairs (Mb).

We generated one mitochondrial genome assembly, 16,730 bp long. The base composition of the final assembly version is A = 28.41%, C = 13.37%, G = 22.71%, T = 35.48%, and consists of 23 transfer RNAs and 13 protein coding genes.

Genome size estimation and quality assessment

The primary assembly consists of 176 scaffolds spanning 1.65 Gb with contig N50 of 16.32 Mb, scaffold N50 of 118 Mb, largest contig of 57.8 Mb, and largest scaffold of 142.4 Mb. The final genome size is close to the estimated values from the Genomescope2.0 k-mer spectrum. The primary assembly has a BUSCO completeness score of 86.0% using the Mollusca gene set, a per base quality (QV) of 65, a k-mer completeness of 67.2 and a frameshift indel QV of 51.43. The alternate assembly has a BUSCO completeness score of 85.20% using the Mollusca gene set, a per base quality (QV) of 59, a k-mer completeness of 68.2 and a frameshift indel QV of 51.43. The scaffold length histogram showed that the largest size differences were between scaffolds 9 and 10 (19.6 Mb) and scaffolds 12 and 13 (19.1 Mb) (Fig. 2D), the latter corresponding to the split indicated by the k-means clustering, which placed scaffolds 1 to 12 into a cluster and scaffolds 13 to 20 into a second cluster.

Comparison to previously published Mytilus genomes

Compared with the most recent assemblies for three other Mytilus species (Table 3), the M. californianus genome assembly produced here is the most contiguous (i.e., contained in the smallest number of scaffolds), has the largest N50 value, and is the longest (1,651,966,901 bp), slightly exceeding M. edulis (1,651,313,236 bp). The M. californianus assembly also has superior BUSCO metrics for core gene completeness (86%), duplication (0.91%), fragmentation (3.3%), and missingness (10.7%). Complete single copy statistics for M. coruscus, M. edulis, and M. galloprovincialis are 81%, 79%, and 71% respectively; duplication statistics are 1.1%, 7.7%, and 5.4%, respectively; fragmentation statistics are 3.4%, 4%, and 4.8%, respectively; missingness statistics are 15.6%, 16.8%, and 24.7%, respectively (Table 3).

Table 3.

BUSCO scores for Mytilus californianus compared with M. coruscus, M. galloprovincialis, and M. edulis.

Mytilus californianus Mytilus coruscus Mytilus edulis Mytilus galloprovincialis
Citation This paper Yang et al. (2021) Unpublished Gerdol et al. (2020)
GenBank ID GCA_021869935.1 GCA_017311375.1 GCA_019925275.1 GCA_900618805.1
Sequencing method/technology PacBio HiFi, Omni-C Oxford Nanopore, Illumina, Hi-C PacBioa, Omni-C PacBio HiFi, Illumina
Assembly length (Gb) 1.65 1.57 1.65 1.28
Sequences 176 4,434 1,119 10,577
GC content 32.57 32.45 32.3 32.14
N50 sequence length (Mb) 118 99.5 116.5 0.21
Complete single copies 4,553 (86%) 4,288 (81%) 4,191 (79%) 3,735 (71%)
Complete + partial single copies 4,730 (89%) 4,468 (84%) 4,403 (83%) 3,988 (75%)
BUSCO duplicated genes 48 (0.91%) 58 (1.1%) 408 (7.7%) 286 (5.4%)
BUSCO fragmented genes 175 (3.3%) 180 (3.4%) 212 (4%) 254 (4.8%)
BUSCO missing genes 567 (10.7%) 827 (15.6%) 892 (16.8%) 1,307 (24.7%)
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Version of PacBio sequencing chemistry not reported.

Discussion

The ecological and economic value of Mytilus species across the globe has motivated the generation of multiple genomic resources for this genus (Murgarella et al. 2016, Gerdol et al. 2020, Li et al. 2020, Yang et al. 2021, BioProject: PRJNA740305). These resources have improved in quality with advances in sequencing and assembly algorithms as can be sSSeen comparing the first mussel genome for M. galloprovincialis produced with Illumina short reads (1.74 million scaffolds, N50 = 2651 bp, Murgarella et al. 2016), to the current M. galloprovincialis assembly produced with PacBio HiFi long reads and Illumina short reads (10,777 scaffolds, N50 = 32.14 Mb, Gerdol et al. 2020). A key advance has been scaffolding assemblies with proximity data from Hi-C or Omni-C libraries, which can greatly increase contiguity. For example, for M. coruscus, a genome assembled from Oxford Nanopore Technology (ONT) long reads and Illumina short reads by Li et al. (2020) is contained in 10,484 scaffolds with an N50 of 898 kb while a genome produced by Yang et al. (2021) using ONT, Illumina, and Hi-C scaffolding reduced scaffold number to 4,434 with a 99 Mb N50. Interestingly, in addition to improvements in contiguity and completeness (as determined by BUSCO metrics), assemblies scaffolded with Omni-C or Hi-C reads have less variation in assembly size (1.57 to 1.65 Gb) than those not scaffolded with proximity data (1.28 to 1.9 Gb), with a possible explanation being that proximity data help resolve highly repetitive areas of the genome, leading to more accurate and precise assembly sizes (Table 3).

Chromosome-scale reference genomes are powerful tools because they provide greater contiguity and completeness to test important ecological and evolutionary hypotheses than a genome assembly that is fragmented and missing genes or other key genomic features. Previous studies using karyotyping have shown that Mytilus mussels, including M. californianus, M. edulis, M. galloprovincialis, and M. trossulus have 14 chromosomes (Ahmed and Sparks 1970; Pérez-García et al. 2014). Yang et al. (2021) commensurately found 90.9% of M. coruscus genome sequence scaffolds in their assembly mapped to 14 chromosomes based on Hi-C proximity data. The Omni-C proximity data we produced here also suggest 14 chromosomes in M. californianus (i.e., 14 major bins along the diagonal containing each proximity read and its mate in Fig. 2C); k-means clustering suggests a similar number of chromosomes (12; Fig. 2D) though the efficacy of this approach may be influenced by the assembly. Mollusc genomes are known to be highly repetitive (Murgarella et al. 2016) and heterozygous (Koehn and Gaffney 1984, Diz and Presa 2008), which complicates the assembly process, and likely explains why we recovered more than 14 genomic scaffolds. Regardless, the assembly we produced here is the most complete of the Mytilus species available and is a powerful resource for comparative and population genomics.

While mussels have biparental inheritance of the mitochondrial genome (Ladoukakis et al. 2002, Mizi et al. 2005) and we therefore would expect to assemble two scaffolds representing the maternal and paternal contributions (Murgarella et al. 2016), we generated only one. Assembling phased genome assemblies is a bioinformatic challenge (Chin et al. 2016, Mostovoy et al. 2016), particularly when heterozygosity is high, parental sequences are not available, and an intrinsic part of pipelines is to purge duplicates. Our single mitochondrial genome assembly therefore may represent either only one of the two genomes or a chimera of the two parental contributions (Table 2). Future research efforts should engage with developing tools for better resolving maternal and paternal assemblies individually for mitochondrial, as well as nuclear, genomes.

Notwithstanding the preceding caveats, the new reference genome for M. californianus will facilitate multiple fields of study. For example, understanding the structure and resilience of the byssal threads may be enhanced by discovering genes encoding the formation of the threads, in a manner paralleling the genome-enabled analyses of structural genes in green mussels, Perna viridis (Inoue et al. 2021). Additionally, the reference genome can be coupled with comparative ecological studies to give a well-rounded understanding of how functional traits diverged in different environments. For example, Pearce and Labarbera (2009) showed that epifaunal species have thicker and more extensive byssal threads than infaunal species, suggesting a correlation with life habits between the two groups of organisms. Furthermore, analyzing the Mytilus genome can expand our knowledge of stress response and immune defense in bivalves, for example elucidating the unique bivalve gene families involved in heat shock proteins (Takeuchi et al. 2016).

Reference genomes also can be useful in multiple applied contexts. First, for example, genomic resources could facilitate husbandry of M. californianus, which has not been substantially developed for aquaculture unlike many other Mytilus species. M. galloprovincialis, the first marine mussel genome to be sequenced (Murgarella et al. 2016), has great value in its native Mediterranean Sea where it constitutes 50% of global EU aquaculture in weight (Robert et al. 2013), but incurs costs as an invasive species in many other parts of the world (Brady and Somero 2006). M. coruscus is economically valuable and popular in Asian cuisine due to its high nutritional content (Li et al. 2020; Zhang et al. 2020). The M. edulis genome was sequenced for the Prince Edward Island growers to develop tools to implement a breeding program to help with the declining population (https://genomecanada.ca/project/breeding-better-blue-mussels-mytilus-edulis-developing-genomic-tools-implementation-modern-and/). Despite growing larger in length and producing twice as much meat as M. edulis in exploratory aquaculture studies (Yamada and Dunham 1989), there is a gap in the literature when it comes to aquaculture studies for M. californianus compared with its sister taxa, which this genome may help redress. Second, with biodiversity conservation as a motivator of the CCGP project, the M. californianus genome can act as a foundation for future work understanding the genetic diversity and population connectivity for planning marine protected areas (MPAs) and MPA networks (Jeffery et al. 2022). This reference genome, coupled with future population genomics study, will deepen our understanding of the evolutionary history of this species and give us a better understanding of how the population is structured, providing a foundation for future genomic studies on ecosystem engineers across the west coast of North America.

Supplementary material

Supplementary material is available at Journal of Heredity online.

Supplementary Fig. S1. Omni-C contact maps for the alternate genome assembly generated with PretextSnapshot.

esac041_suppl_Supplementary_Figure_S1
Click here for additional data file. (18MB, pdf)

Acknowledgments

PacBio Sequel II library prep and sequencing were carried out at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01. Deep sequencing of Omni-C libraries used the Novaseq S4 sequencing platforms at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. We thank Courtney Miller for help assembling Tables 1 and 2, and P. Barber and R. Bay for discussions of mussel genetics. Collections were completed under California Department of Fish and Wildlife permit #D-0023037096-0 and California Department of Parks and Recreation permit #20-820-04. Partial support was provided by Illumina for Omni-C sequencing. Part of this research was conducted using the MERCED cluster (NSF-MRI, #1429783) at the Cyberinfrastructure and Research Technologies (CIRT) at University of California, Merced.

Contributor Information

Lisa X Paggeot, Department of Life & Environmental Sciences, University of California, Merced, Merced, CA 95343, United States.

Melissa B DeBiasse, Department of Life & Environmental Sciences, University of California, Merced, Merced, CA 95343, United States.

Merly Escalona, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States.

Colin Fairbairn, Ecology & Evolutionary Biology Department, University of Santa Cruz, 1156 High St, Santa Cruz, CA 95064, United States.

Mohan P A Marimuthu, DNA Technologies and Expression Analysis Core Laboratory, Genome Center, Department of Biological Sciences, University of California-Davis, Davis, CA 95616, United States.

Oanh Nguyen, DNA Technologies and Expression Analysis Core Laboratory, Genome Center, Department of Biological Sciences, University of California-Davis, Davis, CA 95616, United States.

Ruta Sahasrabudhe, DNA Technologies and Expression Analysis Core Laboratory, Genome Center, Department of Biological Sciences, University of California-Davis, Davis, CA 95616, United States.

Michael N Dawson, Department of Life & Environmental Sciences, University of California, Merced, Merced, CA 95343, United States.

Funding

This study is a contribution of the Marine Networks Consortium (PIs Michael N Dawson, Rachael A. Bay) as part of the California Conservation Genomics Project (PI: H. Bradley Shaffer), with funding provided to the University of California by the State of California, State Budget Act of 2019 (UC Award ID RSI-19-690224).

Data availability

Data generated for this study are available under NCBI BioProject PRJNA777198. Raw sequencing data for sample M0D057914Y (NCBI BioSample SAMN24505264) are deposited in the NCBI Short Read Archive (SRA) under SRR18000156 for PacBio HiFi sequencing data and SRR18000154-55 for Omni-C Illumina Short read sequencing data. GenBank accessions for both primary and alternate assemblies are GCA_021869535.1 and GCA_021869935.1; and for genome sequences JAKFGE000000000 and JAKFGF000000000. The GenBank organelle genome assembly for the mitochondrial genome is CM038905.1. Assembly scripts and other data for the analyses presented can be found at the following GitHub repository: www.github.com/ccgproject/ccgp_assembly.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

esac041_suppl_Supplementary_Figure_S1
Click here for additional data file. (18MB, pdf)

Data Availability Statement

Data generated for this study are available under NCBI BioProject PRJNA777198. Raw sequencing data for sample M0D057914Y (NCBI BioSample SAMN24505264) are deposited in the NCBI Short Read Archive (SRA) under SRR18000156 for PacBio HiFi sequencing data and SRR18000154-55 for Omni-C Illumina Short read sequencing data. GenBank accessions for both primary and alternate assemblies are GCA_021869535.1 and GCA_021869935.1; and for genome sequences JAKFGE000000000 and JAKFGF000000000. The GenBank organelle genome assembly for the mitochondrial genome is CM038905.1. Assembly scripts and other data for the analyses presented can be found at the following GitHub repository: www.github.com/ccgproject/ccgp_assembly.

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