The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes

Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand

The short mackerel Rastrelliger brachysoma (Bleeker 1851) is an important fish in the Gulf of Thailand (GoT). The biology of this species has been intensively studied, but its genetic diversity is little known. The genetic diversity, population genetic structure, and demographic history of this species in the GoT were studied using complete mt control region sequences. The CR sequences of 455 mackerel samples collected from 23 localities at four fishing grounds revealed 333 haplotypes with haplotype diversity (h) per population, ranging between 0.8933 and 1.000, with an average of 0.9781. In turn, the nucleotide diversity (µ) ranged between 0.0119 ± 0.0060 and 0.0333 ± 0.0174, with an average of 0.0220 ± 0.00059.A haplotype network analysis showed that all sequences segregated into two subgroups named, clade I and clade II. Two clades were separated by 26 mutational steps. Each clade formed star-like clusters with many haplotypes derived from a common haplotype. Moreover, an analysis of molecular variance (AMOVA) revealed no significant differences among the studied localities, suggesting the presence of a single population in the GoT. Pairwise differences between samples from different fishing regions also indicated no population structure. Both Tajima's D and Fu's FS statistics were highly significant for the two clades but nonsignificant for the entire population according to a mismatch distribution analysis. These results confirmed that both clades experienced demographic expansion. The estimated expansion times for clade I and clade II were 1,542.307 years (1.5423 ka BP) and 7,602.541 (7.6025 ka BP) years, respectively.

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta)

Simple Summary

Mackerel species are commercially important marine species in Southeast Asia, especially short mackerel and Indian mackerel. However, genomic information about them is still limited. Genome survey of these two mackerel species was reported in this study. Next-generation sequencing and comprehensive bioinformatics were performed to obtain the genetic information. The estimated genome size of both species is around 680 Mbp. The heterozygosity of these species was very similar, while the repeat content for Indian mackerel was slightly higher than for short mackerel. Functional annotation also was reported in this study. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.

Abstract

Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.

Phylogeography of the Japanese scad, Decapterus maruadsi (Teleostei; Carangidae) across the Central Indo-West Pacific: evidence of strong regional structure and cryptic diversity

The Japanese scad Decapterus maruadsi (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome b gene. Genetic homogeneity within the Sundaland region's population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity (π = 0.001-0.003) but high haplotype diversity (h = 0.503-0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by F _ST, AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of D. maruadsi in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.

The complete mitochondrial genome sequence of snake mackerels Paradiplospinus antarcticus (Scombroidei, Gempylidae)

For the first time, we illuminate the complete mitochondrial genome (mitogenome) sequence of the Paradiplospinus antarcticus, which is 16,988 bp in size and contains 13 protein-coding (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region.The base composition of the mitogenome is 26.08% A, 26.77% T, 28.46% C and 18.69% G. Here, we selected 11 genera of species from the mostly monotypic snake mackerel family, including representative Antarctic Paradiplospinus antarcticus that have been identified, and constructed phylogenetic trees to better study the snake mackerel family.

Hydraulic control of tuna fins: A role for the lymphatic system in vertebrate locomotion

The lymphatic system in teleost fish has genetic and developmental origins similar to those of the mammalian lymphatic system, which is involved in immune response and fluid homeostasis. Here, we show that the lymphatic system of tunas functions in swimming hydrodynamics. Specifically, a musculo-vascular complex, consisting of fin muscles, bones, and lymphatic vessels, is involved in the hydraulic control of median fins. This specialization of the lymphatic system is associated with fish in the family Scombridae and may have evolved in response to the demand for swimming and maneuvering control in these high-performance species.

Complete mitochondrial genome analysis of Japanese Spanish mackerel (Scomberomorus niphonius) with phylogenetic consideration

The complete mitochondrial DNA (mtDNA) of Japanese Spanish mackerel (Scomberomorus niphonius) was cloned and sequenced. The total length of the mitochondrial genome is 16,646 bp with an accession number KY228987. Thirty-seven genes are identified in total, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a putative D-loop region. Among these genes, 9 are encoded on the light strand, while others are encoded on the heavy strand. The overall base composition of mitogenome is 28.39% for A, 16.14% for G, 26.52% for T, 28.96% for C, respectively, with a slight higher A + T content (54.91%). The phylogeny analysis based on 18 COI amino acid sequences suggested that S. niphonius and the other two species from Scomberomorus (Scombridae) formed a cluster apart from the one comprising other genus from Scombridae. The complete mitogenome may shed light on the future study of genetic mechanism of Scomberomorus niphonius.

A new classification of viviparous brotulas (Bythitidae) - with family status for Dinematichthyidae - based on molecular, morphological and fossil data

The order Ophidiiformes is a large but not very well known group of fishes, unique among teleosts for showing high diversity in both deep sea and shallow reef habitats. The current classification includes more than 500 species, 115 genera and four families, based primarily on mode of reproduction: viviparous Aphyonidae and Bythitidae vs oviparous Carapidae and Ophidiidae. Since 2004 we revised the bythitid tribe Dinematichthyini, described more than 100 new species and noticed that this group has unique morphological characters, perhaps supporting a higher level of classification than the current status. Here we study the viviparous families phylogenetically with partial mitochondrial (nd4, 16s) and nuclear (Rag1) DNA sequences (2194bp). We use a fossil calibration of otolith-based taxa to calibrate the age of the clade comprising bythitid and dinematicththyid representatives, together with fossil calibrations adopted from previous phylogenetic studies. The separation of the order into two major lineages, the viviparous Bythitoidei and the oviparous Ophidioidei is confirmed. At the familial level, however, a new classification is presented for the viviparous clades, placing Aphyonidae as a derived, pedomorphic member of Bythitidae (new diagnosis provided, 33 genera and 118 species). The current subfamily Brosmophycinae is considered polyphyletic and we propose family status for Dinematichthyidae (25 genera, 114 species), supported by unique, morphological synapomorphic characters in the male copulatory apparatus. Previous use of the caudal fin separation or fusion with vertical fins is ambiguous. Age estimates based on calibrated molecular phylogeny agrees with fossil data, giving an origin within the Cretaceous (between 84 and 104mya) for a common ancestor to Ophidiiformes.

Mitochondrial DNA control region of three mackerels, genus Rastrelliger: structure, molecular diversity and phylogenetic relationship

The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era.

Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae)

In this study, the complete mitochondrial genome of Abbottina rivularis was determined; the phylogenetic analysis with other individuals and closely related species of the gudgeons was carried out. The complete mitogenome of A. rivularis was 16,597 bp in length, which consists of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 2 non-coding regions: (D-loop and OL). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%). This study provides useful data to genetics, conservation and evolution study of the gudgeons.

Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae)

In the present study, the complete mitochondrial genome of the Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) was sequenced and identified, the phylogenetic analysis with other individual of Sarcocheilichthys fishes was carried out. Totally, this genome is 16,679 bp in length, which consists of 13 PCDs, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The total base composition is: 30.05% A, 26.40% T, 26.70% C, and 16.85% G, respectively. These results will provide useful data for species identification and genetics study of Sarcocheilichthys fishes.

Identification and phylogenetic analysis of the mitochondrial genome of Squalidus sp.SX0527 (Cypriniformes: Cyprinidae)

In this paper, we sequenced the complete mitochondrial genome of the Squalidus sp.SX0527 (Cypriniformes: Cyprinidae). The genome is 16,608 bp in size; it contains 22 tRNA genes, 13 PCD genes, 2 rRNA genes, and 2 non-coding regions. The total base composition is: 30.00% A, 25.48% T, 27.67% C, and 16.85% G, respectively. This study will contribute to species identification and natural resources conservation of Squalidus fishes.

The complete mitochondrial genome sequence of Pampus chinensis (Perciformes: Stromateidae)

In this study, the complete mitochondrial genome of Pampus chinensis (Perciformes: Stromateidae) was determined. The mitogenome is 16,535 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall mtDNA nucleotide base composition of P. chinensis is A 29.72%, C 28.10%, G 15.34%, and T 26.84%, with an A + T content of 56.56%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. chinensis may be helpful to the studies on stock evaluation and conservation genetics of P. chinensis resource, as well as molecular phylogeny of Stromateidae.

Description and phylogenetic analysis of the mitochondrial genome of Pseudobagrus ondon Shaw (Siluriformes; Bagridae)

Pseudobagrus ondon is a small benthopelagic freshwater species of family Bagridae. In the present study, the complete mitochondrial genome of P. Ondon has been determined, and phylogenetic analysis with another individual and closely related species are preformed. The complete mitochondrial genome of P. ondon was 16,534 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: a control region (D-loop) and an L-strand replication origin (OL). It indicated that D-loop, ND1, ND2, ND4, ND5 and CYTB may be appropriate markers for studying population as well as conservation genetics.

The complete mitochondrial genome sequence of Microphysogobio tafangensis (Cypriniformes: Cyprinidae)

In the present study, the total mitochondrial genome of Microphysogobio tafangensis (Cypriniformes: Cyprinidae) was determined. The full genome was 16,683 bp in length, which consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The nucleotide composition of M. tafangensis mitochondrial genome was A: 29.38%, G: 17.71%, T: 25. 47% and C: 27.44%.

The complete mitochondrial genome of Pseudobagrus ondon Shaw

In this study, the total mitochondrial genome sequence of Pseudobagrus ondon Shaw was firstly sequenced and determined. The total genome is 16,543 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. These results provide useful data to the natural resources conservation and systematics analysis of P. ondon Shaw.

The complete mitochondrial genome of Pseudobagrus albomarginatus Rendhal: sequencing and analysis

In this study, the total mitochondrial genome sequence of Pseudobagrus albomarginatus Rendhal was firstly sequenced and determined. The total genome is 16,533 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions. The data presented herein would facilitate further investigations of phylogenetic relationships within Bagridae catfishes.

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families

Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families.

A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations

Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.

Complete mitochondrial genome of Pseudorasbora elongata (Cypriniformes: Cyprinidae): sequencing and analysis

In this study, the total mitochondrial genome sequence of Pseudorasbora elongata (Cypriniformes: Cyprinidae) was firstly determined. The genome is 16,587 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. These results will contribute to the natural resources conservation and species identification of P. elongata.

The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae)

In this study, the total mitochondrial genome of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae) was firstly determined. The genome is 16,683 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The overall nucleotide composition of the H-strand of S. sinensis sinensis mitochondrial genome is A: 30.48%, G: 16.65%, T: 26.30% and C: 26.58%, respectively, with an A + T rich feature (56.78%). These results provide useful data to further study of the molecular systematics, species identification and conservation genetics.

Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences

The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.

Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes

The black carp Mylopharyngodon piceus (Cyprinidae), native to eastern Asian, is a large, commercially important fish, and has been introduced to many other countries for variable reasons. In this study, the complete mitochondrial genome sequences from three specimens of black carp were first determined and were used to evaluate the sister relationship between black carp and grass carp (Ctenopharyngodon idellus). Two individuals had a mitogenome of 16,609 bp, while the other was 16,611 bp in length. Similar to most vertebrates, the black carp contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analyses using three different computational algorithms (Maximum Parsimony, Maximum Likelihood, and Bayesian analysis) revealed two distinct clades in subfamily Leuciscinae. However, the sister taxonomic relationship of black carp and grass carp was not observed using sequences of nearly complete mitochondrial genomes, which suggests more nuclear gene markers are needed to resolve the phylogenetic relationship between black carp and grass carp.

Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans

We present the complete sequence of the mitochondrial genome (mitogenome) of the cotton bollworm Helicoverpa armigera. The 15,347-bp mitogenome of H. armigera was arranged in the same order described for all other sequenced lepidopterans, which differs from the most common type found in insects, due to the movement of trnM to a position 5'-upstream of trnI. The gene overlap in the H. armigera mitogenome is totally 23 bp in six locations. The H. armigera mitogenome has a total of 175 bp of intergenic spacer sequences spread over 14 regions ranging in size from 1 to 45 bp. The nucleotide composition of the whole mitogenome of H. armigera is highly A+T biased, accounting for 80.97%, with a slightly positive AT skewness and negative GC skewness, indicating the occurrence of more A than T, C more than G. The protein-encoding genes have typical mitochondrial start codons, except for cox1, which contains the unusual CGA. The cox1, cox2, and nad4 genes have incomplete stop codons (T). The lrRNA and srRNA genes are 1395 and 794-bp long, respectively. All tRNAs have a typical cloverleaf structure of mitochondrial tRNAs, except for trnS1(AGN), the dihydrouridine arm of which could not form a stable stem-loop structure. The H. armigera A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream of trnM.