Analysis of biochemical, genetic, and morphological adaptation focused on metamorphosis from Heliocidaris crassispina based on the transcriptomic and accurate genotyping strategy

Metamorphosis is the vital biological and morphologic process in sea urchins with planktonic larval stage. With complex physiological and biochemical mechanisms demanded during metamorphosis, high mortality is always a problem in the purple sea urchin Heliocidaris crassispina. In our study, the transcriptome of the entire individual was assembled de novo and compared between eight-arm larva (LA) and post-larva (PL) of H. crassispina, aimed to explore the differential regulators associated with metamorphosis. Differential expression genes (DEGs) analysis demonstrated 29,542 DEGs in two groups, with 22,507 significant up-regulated genes and 7035 significant down-regulated genes, respectively. These DEGs may make a difference to cellular components, molecular functions, and biological processes correlated with metamorphosis. Afterward, with the threshold among depths of SNPs, qualities of SNPs, Bonferroni Correction for p-value, minor allele frequency (MAF) values, and minor allele frequency imbalance (AFI), 157 potential positive SNPs associated with metamorphosis were screened from a total of 672,329 SNPs in this RNA-seq. Among them, 8 candidate SNPs were screened and genotyped accurately on SNP loci of 264 PL individuals and 288 LA individuals via Genotyping-in-thousands by sequencing technology (GT-seq), respectively. Subsequent correlation analysis indicated that three SNPs might be closely associated with the threshold trait that metamorphoses rapidly or slowly. More importantly, these data suggest that sea urchin H. crassispina could exhibit a biochemical-level and genetic-level adaptive strategy when facing selection pressure. This study lays a solid foundation for further exploring the molecular mechanism of metamorphosis in purple sea urchin H. crassispina and then provides basic data and reasonable methods to screen and revalidate SNPs for metamorphic traits of purple sea urchin H. crassispina.