Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus

Abstract

Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, 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 forthcoming population genomic data. The genome of C. violaceus is typical of many marine fishes at less than 1 Gb (genome size = 575.6 Mb), and our assembly is near-chromosome level (contig N50 = 1 Mb, scaffold N50 = 16.4 Mb, BUSCO completeness = 93.2%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects, enhancing our knowledge of the population structure of the species and more generally, the efficacy of marine protected areas as a primary conservation tool across California's marine ecosystems.

Keywords: CCGP; California Conservation Genomics Project; marine protected areas.

Fig. 1.

A) Distribution of Monkeyface Prickleback, Cebidichthys violaceus. Monkeyface Pricklebacks are found in the intertidal and subtidal to a depth of 25 m from Southern Oregon, USA, to Northern Baja California, Mexico. The collection site of the sequenced individual, Pacific Grove California, is indicated by the star on the map. Inset is an illustration of C. violaceus (Illustration credit: Andrea Dingeldin). B) A Monkeyface Prickleback, C. violaceus (photo by M.H. Horn) and an image of Franklin Point California at low tide, an example of representative intertidal habitat for the Monkeyface Prickleback. C) Phylogenetic relationships of the nonmonophyletic family Stichaeidae based on 2,100 bp of cytb, 16s, and tomo4c4 genes (Kim et al. 2014). Bayesian posterior probabilities are indicated on nodes. C. violaceus is bolded and the letters after the names are H = herbivory, O = omnivory, C = carnivory. Evolution of herbivory (— — — —) and omnivory (............) are shown. Numbers in parentheses are the number of taxa contained in that branch. Some groups are collapsed into subfamilies. Asterisks indicate that this species (or species in that group) are found in California.

Fig. 2.

Visual overview of genome assembly metrics. A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Cebidichthys violaceus primary assembly. 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 versus light blue area around it shows mean, maximum and minimum GC versus AT content at 0.1% intervals (Challis et al. 2020). 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 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between 2 of such regions.