Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems - PubMed (original) (raw)
Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems
Giacomo Bernardi et al. J Hered. 2022.
Abstract
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.
Keywords: CCGP; California Conservation Genomics Project.
© The Author(s) 2022. Published by Oxford University Press on behalf of The American Genetic Association.
Figures
Figure 1.
Distribution (dark area) of California Sheephead, Semicossyphus pulcher. California Sheephead are found on rocky reefs of California, USA, and Baja California, Mexico, including the isolated offshore Guadalupe island (represented as a dot), and the Sea of Cortez. The collection site of the sequenced individual, Leo Carrillo State Beach, is indicated by the black star on the map. Drawings represent male (top) and female (bottom) California Sheephead (art work by Amadeo Bachar,
).
Figure 2.
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 and frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes. (B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Semicossyphus pulcher primary assembly (fSemPul1). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in grey starting from the outside of the central plot. Dark and light arcs show the scaffold N50 and scaffold N90 values. The central light grey 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 versus light areas around it shows mean, maximum, and minimum GC versus AT content at 0.1% intervals (Challis et al. 2020). (C–D) Omni-C contact maps for the primary (C) and alternate (D) genome assembly generated with PretextSnapshot. Hi-C contact maps translate proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions.
Figure 3.
Distribution of scaffolds of the genome assembly for California Sheephead, Semicossyphus pulcher. Only the largest scaffolds are shown, in decreasing order of size from left to right. Scaffold size is given in megabase pairs (Mb).
References
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