DeBiasse MB et al. (2022), A chromosome-level reference genome for the gia...

ECB-ART-50928

J Hered 2022 Nov 30;1136:689-698. doi: 10.1093/jhered/esac044.

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

DeBiasse MB , Schiebelhut LM , Escalona M , Beraut E , Fairbairn C , Marimuthu MPA , Nguyen O , Sahasrabudhe R , Dawson MN .

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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 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener 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.

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	Fig. 1. Map showing the current known distribution (ca. 2022) of the giant pink sea star, Pisaster brevispinus, from Sitka, Alaska, United States to Ensenada, Baja California, Mexico. The individual sequenced for this study was collected at Terrace Point, Santa Cruz, California on 13 October 2020. The inset shows a photograph of a P. brevispinus sea star at Morro Bay, California. Photo credit: Jerry Kirkhart (https://www.flickr.com/photos/jkirkhart35/423749561/), some rights reserved (https://creativecommons.org/licenses/by/4.0).
	Fig. 2. Visual overview of genome assembly metrics. (A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope 2.0. The bimodal pattern observed corresponds to a diploid genome. K-mers covered at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and 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 Pisaster brevispinus primary assembly (eaPisBrev1). 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. (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 2 such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation. (D) Histogram of the 50 largest P. brevispinus scaffolds. Gray dashed line represents the break point for 2 clusters delimited by k-means clustering of scaffold lengths.
	Fig. 3. Whole genome alignment between the predicted Pisaster ochraceus 22 chromosomes (x axis) and top 23 longest Pisaster brevispinus primary assembly scaffolds (y axis). Blue dots represent areas of sequence alignment in the same direction and green dots represent areas of inverted sequence alignment in P. brevispinus (the query) relative to the P. ochraceus sequence (the reference). Light gray lines indicate chromosome and scaffold boundaries. The total axes are scaled by sequence length contained in top 23 P. brevispinus scaffolds (437.4 Mb) and P. ochraceus chromosomes (398.1 Mb). Each scaffold-to-chromosome alignment block is scaled by the length of the P. ochraceus chromosome (x axis) and the P. brevispinus scaffold (y axis).

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Abdennur, Cooler: scalable storage for Hi-C data and other genomically labeled arrays. 2020, Pubmed