The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

Abstract

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

Particular gene order and complete mitochondrial genome of Beach conger (Conger japonicus)

“…In addition, the overall base composition is T 27.3%, C 23.6%, A 32.0%, and G 17.0%. The A + T content is higher than the G + C content, which is similar to other fishes (Cheng et al, 2012). An anti-G bias is ascertained in the third position of protein-coding genes, which is similar to other vertebrate mitogenomes (Cheng et al, 2011;Jin et al, 2012).…”

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD‐seq for the small yellow croaker (Larimichthys polyactis)

“…In addition, the complete mitochondrial genome of the small yellow croaker is also available in GenBank (Cheng et al . ). Nevertheless, the limited source of markers has somehow constrained genetic studies during the last two decades, for instance, most of population genetic structure and demographic history studies of L. polyactis were based on a handful of microsatellite markers, mitochondrial sequence analysis, amplified fragment length polymorphism (AFLP) or internal and external features of otoliths, which obtained discrepant or even conflicting results (Han et al .…”

Complete mitochondrial genome of Japanese bigeye (Pristigenys niphonia): genome characterization and phylogenetic analysis

“…The base composition of Japanese bigeye is 24.9% of T, 30.6% of C, 27.7% of A, and 16.8% of G. The A þ T (52.6%) content is higher than G þ C (47.4%) content, which is similar to other fishes (Cheng et al 2011a;Jin et al 2012). Furthermore, the anti-G bias is ascertained in the third position of protein-coding genes, which brings Red bigeye in line with other vertebrate mitogenomes (Cheng et al 2012a;Jin et al 2013). The two ribosomal RNA genes 12S rRNA (954bp) and 16S rRNA (1703bp) are located on the heavy strand between tRNA Phe and tRNA Leu (UUR), and being separated by tRNA Val gene.…”