Characterization of the Complete Mitochondrial Genome Sequences of Three Croakers (Perciformes, Sciaenidae) and Novel Insights into the Phylogenetics

Abstract

The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.

The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

“…Our phylogenetic tree (Fig. 2a) showed Lobotiformes was more related to Sciaenidae than to Tetraodontiformes, which supported the results of some previous studies [5, 6]. Furthermore, the divergence time between Lobotiformes and Sciaenidae was inferred to be 82.9 mya (Fig 2a).…”

“…The nucleotide sequences on the four-fold degenerate (4d) site of those single-copy gene families were used to construct the maximum likelihood (ML) tree. The phylogeny of the seven orders was found consistent with the previous study [5, 6]. Order Perciformes was identified as the early branch to other orders in Eupercaria, and the divergent time was estimated 101.9 million years ago (mya).…”

“…[4], agreed with this phylogeny by investigating. However, more recently Lobotiformes was reported to be more closely related to Sciaenidae than Tetraodontiformes based on complete mitochondrial genome [5]using and transcriptomic data [6]. Furthermore, fourteen families of Eupercaria included in order-level incertae sedis , which are called “new bush at the top”, were not arranged to explicit orders and interrelationships among them was a long-term issue [7].…”

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

“…The whole mitochondrial genome of the freshwater drum had an AT content of 53.6% and a GC content of 46.4%. This is relatively similar to the base composition of most other Sciaenidae species (52%-56%), with the exception of species in the genus Johnius, which have a base composition different from other sciaenids (Fonseca et al 2014, Xu et al 2015, Yang et al 2018.…”

“…Mt genomes, which usually contain 12-13 proteincoding genes (PCGs), provide much higher phylogenetic resolution than single-gene markers, so they are becoming an increasingly popular tool for resolving phylogenetic debates (Der Sarkissian et al 2015, Lan et al 2017, Bourguignon et al 2018. Although a number of studies relied on this approach to study the phylogeny of the Sciaenidae (or selected sciaenid taxa) (Cheng et al 2010, Xu et al 2015, Zhao et al 2015, Lin et al 2017, Yang et al 2018, the resolution of the mitochondrial phylogenomics approach is still hampered by the limited number of mt genomes available for this family.…”