An update of the salmon louse (<i>Lepeophtheirus salmonis</i>) reference genome assembly

Joshi, Jay; Flores, Anne-Marie; Christensen, Kris A.; Johnson, Hollie; Siah, Ahmed; Koop, Ben F.

doi:10.1093/g3journal/jkac087

“…The contig N50 length we obtained here was greater than 33 out of 35 available genome assemblies for Copepoda in NCBI Genome database [42]. The two copepod assemblies with greater contig N50 length than ours are based on Oxford Nanopore sequencing and their samples are taken from wild outbred populations [46,47]. The contig N50 of our genome was also longer than 151 out of 154 published genome assemblies of marine invertebrates in a recent survey [45].…”

Section: Chromosome-level Genome Assemblymentioning

confidence: 74%

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

Du

¹

,

Gelembiuk

²

,

Moss

³

et al. 2023

Preprint

0

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Background: Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as the food source for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genomic mechanisms underlying this highly invasive and adaptive capacity. Results: Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb) was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transporter gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transporter genes and significant clustering of these genes on each chromosome. Conclusions: This genome represents one of the most contiguous copepod genomes to date and among the highest quality of marine invertebrate genomes. As such, this genome provides an invaluable resource that could help yield fundamental insights into the ability of this copepod to adapt to rapid environmental transitions.

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“…The contig N50 length we obtained here was greater than 33 out of 35 available genome assemblies for Copepoda in NCBI Genome database [42]. The two copepod assemblies with greater contig N50 length than ours are based on Oxford Nanopore sequencing and their samples are taken from wild outbred populations [46,47]. The contig N50 of our genome was also longer than 151 out of 154 published genome assemblies of marine invertebrates in a recent survey [45].…”

Section: Chromosome-level Genome Assemblymentioning

confidence: 80%

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

Du

¹

,

Gelembiuk

²

,

Moss

³

et al. 2023

Preprint

0

View full text Add to dashboard Cite

Background: Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as the food source for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genomic mechanisms underlying this highly invasive and adaptive capacity. Results: Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb) was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transporter gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transporter genes and significant clustering of these genes on each chromosome. Conclusions: This genome represents one of the most contiguous copepod genomes to date and among the highest quality of marine invertebrate genomes. As such, this genome provides an invaluable resource that could help yield fundamental insights into the ability of this copepod to adapt to rapid environmental transitions.

show abstract

“…The contig N50 length we obtained here was greater than 33 out of 35 available genome assemblies for copepod species in Genome database [53]. The two copepod assemblies with greater contig N50 length than ours are based on Oxford Nanopore sequencing and their samples are taken from wild outbred populations [58,59]. The contig N50 of our genome was also longer than 151 out of 154 published genome assemblies of marine invertebrates in a recent survey [42].…”

mentioning

confidence: 74%

The genome architecture of a copepod invading novel habitats

Du,

Gelembiuk,

Moss

et al. 2023

Preprint

1

0

View full text Add to dashboard Cite

With climate change, salinity is rapidly changing in marine and freshwater habitats throughout the globe. In addition, many of the most destructive aquatic invaders are crossing salinity boundaries. Populations of the copepod Eurytemora affinis species complex are numerically dominant and highly invasive, with the exceptional capacity to rapidly invade and adapt to novel salinities. Prior studies have found striking patterns of parallel adaptation in E. affinis complex populations, with selection acting on the same sets of ion transporter genes during independent saline to freshwater invasions. Our chromosome-level genome of Eurytemora carolleeae (Atlantic clade of the E. affinis complex) revealed a peculiar genome architecture that might contribute to its remarkable capacity to acclimate and evolve during salinity invasions. We assembled the highest quality copepod genome to date, using high-coverage PacBio and Hi-C sequencing of an inbred line generated through 30 generations of full-sib mating. Our new genome consisted of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb) anchored onto four chromosomes. Of its predicted 20,262 protein-coding genes, we found an extraordinary expansion of ion transporter gene families based on a comparative analysis of 13 arthropod genomes, with many of these expansions being recent. Notably, we found extreme CpG depletion of the ion transporter gene bodies, indicating high rates of methylation at these genes and suggesting transcriptional robustness of ion transporter gene regulation. This high-quality genome provides an invaluable resource that could help yield fundamental insights into the capacity of populations to expand their ranges into novel habitats.

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An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly

Cited by 10 publications

References 31 publications

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

The genome architecture of a copepod invading novel habitats

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