The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae

Abstract

Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea.

Sequencing of the Complete Mitochondrial Genome of the Big Brown Mactra Clam, Mactra grandis (Venerida: Mactridae)

“…With the continuous decrease in the cost of sequencing high-quality genomes, an increasing number of mitochondrial genomes for mollusks have been reported. These contributions have significantly enriched studies in taxonomy, germplasm research, and investigations into adaptive evolution [1][2][3][4]. On one hand, molluscan mitogenomes offer valuable molecular insights for biological taxonomy research, encompassing conserved sequences of functional genes and gene arrangements among closely related species [5][6][7].…”

Comparative Mitogenome Analyses of Fifteen Ramshorn Snails and Insights into the Phylogeny of Planorbidae (Gastropoda: Hygrophila)

“…Studying molecular variation and phylogenetics among closely related species will provide insights into basic biological questions, such as those pertaining to taxonomy [1], genetic diversity [2], evolution [3], and interspecific interaction relationships [4]. With the development of high-throughput sequencing and bioinformatic analyses, the bulk of molecular data has become efficient and economical to obtain, which allows them to be applied to the resolution of the longstanding questions posed by traditional techniques [5].…”

“…Genes underlined are on the minor strand; genes not underlined are on the major strand; tRNA genes are indicated with one-letter corresponding amino acids 2. INC: intergenic nucleotides; positive values indicate gaps and negative values indicate overlapped nucleotides between adjacent genes.…”