Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

Abstract

The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by ND6 and eight transfer RNA (tRNA) genes. The C. camerunensis mitochondrial genome is AT biased (56.89%), as showcased in other Clarias species. The comparative analyses revealed that most of the Clarias species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of C. camerunensis folded into the distinctive cloverleaf secondary structure, except trnS1. The placement of the conserved domains in the control region was similar in all the Clarias species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all Clarias species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of Clarias species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (C. dussumieri) and African species (C. camerunensis and Clarias gariepinus) took place during the Paleogene, as well as the South Chinese species (Clarias fuscus) and Sundaland species (Clarias batrachus) splits from the Indochinese species (Clarias macrocephalus) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of Clarias species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of Clarias species in African and Asian countries.

Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids

“…A comparative study of the other two Coptodon mitogenomes revealed that the AT skew varied from 0.027 to 0.028, and the GC skew ranged from 0.299 to 0.306 ( Table 2 ). A similar pattern of the nucleotide composition and AT biases were reported in previously characterized fish mitogenomes [ 90 , 91 ]. The genetic diversity detected in Coptodon mitogenomes could be related to their evolutionary process and energy metabolism, as demonstrated in other fish [ 92 ].…”

“…zillii mitogenomes contained tandem repeats. The conserved block locations (CSBD, CSBI, CSBII, and CSBIII) were determined to be comparable in both C. camerunensis and C. zillii , as documented in other teleost fishes [ 90 , 91 , 97 ]. The length of the CSBII block was the longest (52 bp) when compared to the other blocks, which were CSBD (27 bp), CSB-I (41 bp), and CSBIII (43 bp).…”

“…It was possible to identify the inter- and intra-specific differences among Coptodon species using these variable nucleotides. As demonstrated in other species, similar studies on conserved domains may be required to understand the replication and transcription of the mitochondrial genome [ 90 , 91 ].…”

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean

“…Comparative analysis of P. erumei mitogenomes demonstrated an AT skew range of 0.076 to 0.077, and a GC skew range of −0.323 to −0.328 (Table 2). This consistent nucleotide composition pattern and AT bias were also observed in other previously described fish mitogenomes [60,61]. The genetic variations identified within the Psettodes mitogenome may be tied to their evolution-ary progression and energy metabolism, echoing findings in other fish species [62].…”

Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon

“…In addition, several small- to large-scale DNA barcoding attempts have been made to illuminate the genetic diversity of catfishes around the world, including in Africa [ 35 , 36 , 37 , 38 ]. A recent study generated the first mitochondrial genome of C. camerunensis and elaborated the diversification of Clarias species in Africa and the Asian continent [ 39 ].…”