The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: Purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes

Molina-Quirós, José Luis; Hernández, Sebastián; Baeza, Juán Antonio

doi:10.1016/j.gene.2022.146847

Cited by 6 publications

(3 citation statements)

References 56 publications

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“…It is crucial to emphasize that these incomplete stop codons may potentially be completed with TAA during RNA processing, as suggested in previous studies [62]. As observed in other fish species, the identified genetic variations could lead to the independent selection of protein-coding genes (PCGs) [63]. These PCGs play essential roles in oxidative phosphorylation, ATP synthesis, and the encoding of proteins involved in electron transport pathways.…”

Section: Protein-coding Genesmentioning

confidence: 71%

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Mitogenomic Architecture and Phylogenetic Relationship of European Barracuda, Sphyraena sphyraena (Teleostei: Sphyraenidae) from the Atlantic Ocean

Kundu,

Kim,

Lee

et al. 2023

Fishes

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The collective understanding of global-scale evolutionary trends in barracuda mitogenomes is presently limited. This ongoing research delves into the maternal evolutionary path of Sphyraena species, with a specific focus on the complete mitogenome of Sphyraena sphyraena, sourced from the Atlantic Ocean through advanced next-generation sequencing. This mitogenome spans 16,841 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. Notably, the mitogenome of S. sphyraena exhibits a preference for AT-base pairs, constituting 55.06% of the composition, a trait consistent with a similar bias found in related species. Most protein-coding genes initiate with an ATG codon, with the exception of Cytochrome c oxidase I (COI), which begins with a GTG codon. Additionally, six PCGs terminate with a TAA codon, COI with AGA, while six others exhibit incomplete termination codons. In the S. sphyraena mitogenome, the majority of transfer RNAs exhibit typical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the D-loop regions of six Sphyraenidae species reveals that the CSB-I block extends to 22 base pairs, surpassing other blocks and containing highly variable sites. Both maximum-likelihood and Bayesian phylogenetic analyses, using concatenated 13 mitochondrial PCGs, distinctly separate all Sphyraenidae species. The European Barracuda, S. sphyraena, demonstrates a sister relationship with the ‘Sphyraena barracuda’ group, including S. barracuda and S. jello. In conclusion, this study advances our understanding of the evolutionary relationship and genetic diversity within barracudas. Furthermore, it recommends comprehensive exploration of mitogenomes and broader genomic data for all existing Sphyraenidae fishes, providing invaluable insights into their systematics, genetic characterization, and maternal evolutionary history within marine environments.

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Section: Protein-coding Genesmentioning

confidence: 71%

“…x FOR PEER REVIEW 9 of 18 genes (PCGs)[63]. These PCGs play essential roles in oxidative phosphorylation, ATP synthesis, and the encoding of proteins involved in electron transport pathways.…”

mentioning

confidence: 99%

Mitogenomic Architecture and Phylogenetic Relationship of European Barracuda, Sphyraena sphyraena (Teleostei: Sphyraenidae) from the Atlantic Ocean

Kundu,

Kim,

Lee

et al. 2023

Fishes

View full text Add to dashboard Cite

show abstract

“…These incomplete stop codons could potentially be completed with TAA during RNA processing, as previously suggested [63]. As observed in other fish species, the identified genetic disparities might lead to the independent selection of PCGs [64]. PCGs play pivotal roles in oxidative phosphorylation, ATP synthesis, and the encoding of proteins within the electron transport pathways.…”

Section: Protein-coding Genesmentioning

confidence: 74%

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

Kundu,

Palimirmo,

Kang

et al. 2023

Biology

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The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35−10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

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Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes

Halasan,

Lin

2024

Org Divers Evol

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The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: Purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes

Cited by 6 publications

References 56 publications

Mitogenomic Architecture and Phylogenetic Relationship of European Barracuda, Sphyraena sphyraena (Teleostei: Sphyraenidae) from the Atlantic Ocean

Mitogenomic Architecture and Phylogenetic Relationship of European Barracuda, Sphyraena sphyraena (Teleostei: Sphyraenidae) from the Atlantic Ocean

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

Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes

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