Structure and evolution of the complete mitochondrial genome of the freshwater drum, Aplodinotus grunniens (Actinopterygii: Perciformes: Sciaenidae)

Abstract

R. 2020. Structure and evolution of the complete mitochondrial genome of the freshwater drum, Aplodinotus grunniens (Actinopterygii: Perciformes: Sciaenidae). Acta Ichthyol. Piscat. 50 (1): 23-35.Background. Overfishing and habitat degradation caused a decline of populations of many fish species belonging to the speciose family Sciaenidae. A reliable taxonomic framework is a prerequisite for implementing effective stock management and conservation measures, but phylogeny and taxonomy of the Sciaenidae remain poorly resolved. As traditionally used morphological and single gene-based molecular markers carry a too limited phylogenetic signal for the task, mitochondrial phylogenomics may be a more suitable tool. The freshwater drum, Aplodinotus grunniens Rafinesque, 1819, is one of the few Sciaenidae species that live in freshwater habitats, which makes it an important model for studying the phylogeny and evolution of Sciaenidae. Material and methods. We sequenced and characterized its mitogenome, and reconstructed the phylogeny of Sciaenidae using mitogenomes of 28 species. Results. The architecture of the mitogenome (16487 bp in length) is standard for this family, and three typical elements were identified in the control region: extended termination associated sequences, central conserved region, and conserved sequence block. Poor availability of sciaenid mitogenomes (especially those belonging to different lineages) prevented us from resolving the phylogeny of this family with confidence. Notably, our results indicate that Larimichthys and Collichthys species may belong to a single genus, and we suspect that the mitogenome of Chrysochir aureus (Richardson, 1846) has been misidentified taxonomically, and urge its resequencing. Conclusion. The sequencing of additional mitogenomes belonging to non-represented and poorly represented lineages is needed to facilitate the understanding of phylogeny and taxonomy of Sciaenidae.

Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama

“…Johnius was the earliest genus to be evolved within the family according to a phylogenetic analysis and could be a prove of relatively slower rate of change in Sciaenidae over time 48 . However, an alternate hypothesis, discussed in Wen et al 49 , posits that this genus may be of recent origin. Incorporating nuclear genomic data could be instrumental in accurately establishing its position.…”

The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis

“…Phylogenetic studies based on molecular data have become a hot topic since the 21st century. At first, a limited set of mitochondrial and nuclear genes were used as markers in the phylogeny of Sciaenidae fish [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. However, they may not be reliable because of the introgression, saturation, or selection of mitochondrial genes [ 18 ].…”

“…For example, Lo et al performed a comprehensive study based on the cyt b , COⅠ , RAG1 , RH , EGR1 , and EGR2B genes of Sciaenidae and revealed that the genus Argyrosomus was the basal genus of the Western Pacific species [ 6 ]. However, the study based on mtDNA genomes supported that the genus Argyrosomus and the genus Sciaenops formed a sister lineage, whereas the genus Miichthys occupied the basal position within the West Pacific lineage [ 17 ]. Therefore, to date, the phylogenetic status of the Sciaenidae family has not been ambiguously resolved, mainly because of the application of the limited amount of genetic data for the study.…”

Sequencing and analysis of the mitochondrial genome of Pennahia anea (Bloch, 1793) (Perciformes: Sciaenidae)

“… 2017 ; Wen et al. 2020 ). The mitogenome reported from this study might be helpful for future studies that deal with the genetic diversity of P. anea .…”