Phenotype-Specific Mitochondrial Genomic Signatures and Multi-Factorial Speciation in Tropical Sea Urchins with Spine Color Polymorphism
Description
The complete mitochondrial genome of the tropical sea urchin Echinometra mathaei (de Blainville, 1825) with three different spinal color phenotypes (brown, green and white) collected from the coastal waters of Sanya was sequenced. The length of mitochondrial genome of the brown-spined, the green-spined and the white-spined sea urchin is 15696 bp, 15696 bp and 15693 bp, respectively. The three genomes each contain 13 protein coding genes, 22 tRNA genes and 2 rRNA genes. Based on the 16 sequences with high similarity obtained from NCBI and all coding sequences of the three mitochondrial genome sequences, the base composition was analyzed, and the phylogenetic tree was constructed by maximum likelihood method. The results indicated that all three phenotypes exhibited a significant A+T bias, which is consistent with the general nucleotide composition patterns observed in sea urchins. The A-T skew values show that the brown-spined sea urchin is -0.0556, the green one is -0.0554, and the white one is -0.0563, indicating a slight asymmetry in the distribution of A/T between DNA strands. Phylogenetic analysis showed that the three phenotypes and two species of Echinometra genus formed a good monophyletic evolutionary clade, but there was a certain genetic differentiation among the three sea urchins. The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] (https://www.ncbi.nlm.nih.gov/) under the accession no. PX252144 (brown-spined Echinometra mathaei) – PX252145 (green-spined E. mathaei) – PX252146 (white-spined E. mathaei). The raw genome sequence data has been publicly stored in the SRA database of the NCBI. The bioproject data numbers are PRJNA1312048 (brown-spined E. mathaei) – PRJNA1312050 (green-spined E. mathaei) – PRJNA1312056 (white-spined E. mathaei). The biosample data numbers are SAMN50847818 (brown-spined E. mathaei) – SAMN50847837 (green-spined E. mathaei) – SAMN50848074 (white-spined E. mathaei). The SRA data numbers are SRR35197848 (brown-spined E. mathaei) – SRR35197869 (green-spined E. mathaei) – SRR35197872 (white-spined E. mathaei).
Files
Steps to reproduce
In this experiment, the three Echinometra mathaei sequences from Sanya, Hainan, China (18 ° 11.7 'n, 109 ° 29.6' e) and all coding sequence files from 16 similar mitochondrial genomes of sea urchin obtained after blast alignment in NCBI were used to analyze the base composition and construct the phylogenetic tree (maximum likelihood method) using MEGA-X software. The relevant files are as follows: All 16 TXT suffix files are all coding sequence files in mitochondria of 16 sea urchin species downloaded from NCBI. The three files with the suffix of FASTA are all the coding sequence files in the mitochondria of Echinometra mathaei with three kinds of Echinometra colors. The all.meg file is the comparison result file after the above sequences are compared by MEGA-X software. Figure.docx file contains "Figure 1. mitochondrial genes of brown spined (a), green spined (b) and white spined (c) Echinometra mathaei" and "Figure 2. maximum likelihood (ML) phylogenetic tree constructed from complete mitochondrial genome sequences of three spined colored Echinometra sea urchins" The table.docx file contains "Table 1. genes used in mitochondrial sequence alignment analysis" and "Table 2. nucleoside composition analysis of multiple sea urchin specialties"
Institutions
- Hainan Tropical Ocean UniversityHainan, Sanya