Characterization and phylogenetic analysis of the complete mitochondrial genome from Rock Scallop (Crassadoma gigantea) using next-generation sequencing

Abstract

2018) Characterization and phylogenetic analysis of the complete mitochondrial genome from Rock Scallop (Crassadomagigantea) using next-generation sequencing, ABSTRACTIn this study, the complete 18,495 bp mitochondrial genome was determined from Rock scallop (Crassadoma gigantea) using next-generation sequencing technology. The complete mitochondrial genome contained 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, 23 transfer RNA genes, without ATP8 and D-loop, which was similar with most mitochondrial genomes of marine bivalve molluscs. Gene annotations, including gene order, genetic code, start and stop codons and codons bias, were identified. Phylogenetic tree was constructed using Neighbor-Joining (NJ) method based on the PCGs showed the present species clustered within the Pteriomorphia clade. This work should be of importance not only for the better understanding of the relationships within Pectinidae, but also for the development of useful genetic markers in Rock scallop aquaculture and restoration efforts. ARTICLE HISTORY

Complex Mitogenomic Rearrangements within the Pectinidae (Mollusca: Bivalvia)

“…The full mitogenome contains 13 Protein Coding Genes (PCGs; including an atp8, reported as missing for many bivalves; [11][12][13]15]), 23 tRNAs, and 2 rRNAs (Fig. 1, Table 1).…”

“…This, however, does not seem to be correlated to sequence similarities among PCGs [12]. Furthermore, like most bivalves, most pectinid mitochondrial genomes contain several in ated non-coding regions, some of which are hypothesized to function as control regions [11][12][13]15], although it remains controversial whether several control regions within a mitogenome could provide normal function [15].…”

“…Gene rearrangements are most common for tRNAs. Several pectinids contain extra tRNAs beyond the essential 22 needed for mitochondrial translation, either duplicated genes, or genes encoding for the same amino acid, but using a different anticodon [13][14][15][16]. However, even more species contain fewer than 22 mitochondrial tRNAs [11,12,14,17,18], possibly coming from annotation errors, which might be the result of modi ed tRNA secondary structure, common in other mollusks [19][20][21].…”

“…However, even more species contain fewer than 22 mitochondrial tRNAs [11,12,14,17,18], possibly coming from annotation errors, which might be the result of modi ed tRNA secondary structure, common in other mollusks [19][20][21]. Similarly, atp8 genes were reported earlier as missing from most bivalves, including pectinids [11][12][13]15], although reannotation efforts revealed its presence in several species [16,22,23]. The di culty of annotating the atp8 gene is thought to stem from the poorly conserved sequence of this gene in bivalves [24][25][26].…”

“…Phylogenies based on full mitogenomes have shown their utility in disentangling evolutionary relationships that were controversial when investigated using only a few genes [38][39][40][41]. There are a few examples of pectinid phylogenies based on complete mitogenomes [12,13,17,22,23], however, most of these studies rely solely on genetic distance-based methods (except: [17,22]), without considering the differences in substitution rates among different mitochondrial genes. Despite the diversity of approaches, some phylogenetic relationships remain to be resolved, for example, those within the Chlamydinae subfamily.…”