Ketchum RN et al. (2022), A Chromosome-level Genome Assembly of the Highl...

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Genome Biol Evol 2022 Oct 07;1410:. doi: 10.1093/gbe/evac144.

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A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.

Ketchum RN , Davidson PL , Smith EG , Wray GA , Burt JA , Ryan JF , Reitzel AM .

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Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.

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	Fig. 1. Echinometra sp. EZ Hox cluster organization is exactly the same as the organization of the Strongylocentrotus purpuratus Hox cluster in terms of membership and orientation. The names on the S. purpuratus Hox genes reflect the names assigned in an earlier study (Cameron et al. 2006). Except for Hox1 and Evx, we omitted names on the E. sp. EZ Hox genes to reflect the uncertainty of the orthology of echinoderm Hox genes relative to the vertebrate Hox genes of the same name (supplementary fig. 3, Supplementary Material online).
	Fig. 2. Chemical defensome genes in five species of sea urchin: Echinometra sp. EZ, Lytechinus variegatus, Strongylocentrotus purpuratus, Heliocidaris erythrogramma, and Heliocidaris tuberculata. Genes were identified by using HMMER searches with PFAM profiles. The gene families were then grouped by their role in the chemical defensome. The colors in the disk represent the PFAM ID and the size of the disk slice represents the number of genes in each respective gene family group. The total number of genes in each group family is represented underneath the disk. As the DNA-binding domain (PF00105) and the ligand-binding domain (PF00104) are likely to be picked up in most nuclear receptor genes, the values under each of the nuclear receptor disks represent the number of unique hits. PFAM groups included in this analysis were from Goldstone et al. (2006) and the grouping of PFAMs into categories followed Eide et al. (2021).
	Fig. 3. Positive selection results based on comparing noncoding elements of Echinometra sp. EZ to Heliocidaris erythrogramma and Heliocidaris tuberculata with Lytechinus variegatus as the outgroup. The plots presented include sites that show evidence of positive selection in all three sea urchin species and the title of each column is the corresponding gene name in the S. purpuratus genome. The x-axis is the distance of the site to the translation start site of the gene (negative is upstream and positive is downstream) and the y-axis is the zeta score (ratio of substitution rate of query to neutral substitution rate). Colored points are sites which have a zeta score ≥ 1.25 and a P-value ≤ 0.05.

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