The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

Abstract

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus

“…The phylogenetic topology showed that the 12S rRNA gene fragment of our assembled mitogenome was grouped in genus Cociella sub-branch, while the previously reported one (MH521260) was clustered with Grammoplites scaber (Fig. 2), which confirmed that the mitogenome reported in Cui et al (2019) should be mislabeled. We also detected possible polyphyletic relationships in the investigated species.…”

“…The complete mitochondrial genome of C. crocodilus was 16 648 bp in size. Phylogenetic analyses revealed that the assembled C. crocodilus genome in our study were highly differentiated with the previously reported one (MH521260) in Cui et al (2019) (Fig. 1d).…”

“…crocodilus genome in our study were highly differentiated with the previously reported one (MH521260) in Cui et␣al . (2019) (Fig. 1d).…”

“…2), which confirmed that the mitogenome reported in Cui et␣al . (2019) should be mislabeled. We also detected possible polyphyletic relationships in the investigated species.…”

Characterization of the Complete Mitochondrial Genome of Schizothorax kozlovi (Cypriniformes, Cyprinidae, Schizothorax) and Insights into the Phylogenetic Relationships of Schizothorax

“…In this study, the A + T content was higher than the G + C content; A had a higher abundance than T so AT-skew was 0.08, and C had a higher occurrence than G so GC-skew was −0.20. Numerous studies have shown that almost all postnatal animals including fishes are characterized by AT bias, indicating that the AT-rich regions might represent the origin of replication and be more easily changed in evolution [ 54 , 55 ]. Generally, the strand skew biases were found to have a negative AT skew and positive GC skew.…”