Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

Background

Thoracotremata belong to the large group of "true" crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.

Methods

Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).

Results

The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.

Selection in coral mitogenomes, with insights into adaptations in the deep sea

Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean's surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject to selection pressures at greater depths to meet the metabolic demands of that environment. Here, we use a phylogenomic framework combined with codon-based models to evaluate whether mt protein-coding genes (PCGs) associated with cellular energy functions are under positive selection across depth in three groups of corals: Octocorallia, Scleractinia, and Antipatharia. The results demonstrated that mt PCGs of deep- and shallow-water species of all three groups were primarily under strong purifying selection (0.0474 < ω < 0.3123), with the exception of positive selection in atp6 (ω = 1.3263) of deep-sea antipatharians. We also found evidence for positive selection at fifteen sites across cox1, mtMutS, and nad1 in deep-sea octocorals and nad3 of deep-sea antipatharians. These results contribute to our limited understanding of mt adaptations as a function of depth and provide insight into the molecular response of corals to the extreme deep-sea environment.

The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura

A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.

Complete mitochondrial genome of a sea cucumber, Euapta godeffroyi (Echinodermata, Holothuroidea, Apodida, Synaptidae)

We determined the complete mitochondrial genome sequence of a holothurian Euapta godeffroyi belonging to the order Apodida. The complete mitogenome of E. godeffroyi was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes. The maximum likelihood (ML) phylogenetic tree placed E. godeffroyi as the sister group to chiridotid species and supported the monophyly of the order Apodida.

The First Complete Mitochondrial Genome of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) and Phylogenetic Relationships within Infraorder Brachyura

Characterizing the complete mitochondrial genome (mitogenome) of an organism is useful for genomic studies in taxonomy and evolution. The mitogenomic characteristics of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) have never been studied. The present study decodes the first mitogenome of E. crenata by high-throughput sequencing (HTS). The length of the mitogenome is 15,597 bp, and it contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL), and 22 transfer RNA genes. There are 14 and 23 genes observed on the heavy and light strands, respectively. E. crenata possesses a trnH-cac translocation, with the trnH-cac shifted between trnE-gaa and trnF-ttc instead of the usual location between nad5 and nad4 in decapods. Phylogenetic analyses based on the current dataset of 33 Brachyuran mitogenomes indicate that E. crenata. is closely related to Ashtoret lunaris of Matutidae. The similar codon usage and rearrangements in the two species provide evidence for their close phylogenetic relationship. Positive selection analysis showed that one residue located in cox1 was identified as a positively selected site with high BEB value (>95%), indicating that this gene was under positive selection pressure. This study is the first complete mitogenome record for the family Goneplacidae, and the results obtained may improve the understanding of the phylogeny of Goneplacidae in Brachyura.

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae)

Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.

The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position

The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.

Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.

Scientific and technological progress in the microbial exploration of the hadal zone

The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.

The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold

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P. shioyasakiensis D1497converted more substrate into biomass at low temperature.

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P. shioyasakiensis D1497 prefered to use codons with A/T in the third position.

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The energy metabolism related genes were down regulated in cold environment.

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P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold.

Genome sequencing of Pseudoalteromonas shioyasakiensis D1497, a psychrophile from the Yap trench, revealed that it contained a circle chromosome of 3,631,285 bp with 40.94% GC content and prefered to use codons with A/T in the third position. Additionally, the relative synonymous codon usage (RSCU) values indicated the codons with A and T in the third position were always the most used. Cultivation of P. shioyasakiensis D1497 presented lower substrate consumption rate, higher ATP pool and higher conversion rate of biomass per unit substrate consumed at low temperature (15 °C) than that of the room temperature (25 °C) culture. Comparative transcriptomic analysis revealed that the mRNA abundance of energy metabolism related genes was decreased in 15 °C culture compared with that of 25 °C culture. In addition to its codon usage biases profile, P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold, converting more carbon source into biomass in cold environment.

Complete mitochondrial genome of a tropical sea cucumber, Stichopus chloronotus

In this study, we report the complete mitochondrial genome of Stichopus chloronotus. The mitogenome was 16,247 base pairs (58.55% A + T content) in length, comprising a total of 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. To resolve the phylogenetic position of S. chloronotus, we analyzed all mitochondrial protein-coding genes from 27 species within the Echinodermata. The results showed that S. chloronotus belonged to the family Stichopodidae and was more closely related to tropical Stichopus species (S. horrens and S. monotuberculatus) than to other species. Our results will be useful for evolutionary analysis of sea cucumber species.

The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea

The deep-sea environment is characterized by darkness, hypoxia, and high hydrostatic pressure. Mitochondria play a vital role in energy metabolism; thus, they may endure the selection process during the adaptive evolution of deep-sea organisms. In the present study, the mitogenome of Phymorhynchus sp. from the Haima methane seep was completely assembled and characterized. This mitogenome is 16,681 bp in length and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of most sequenced conoidean gastropods. Some special elements, such as tandem repeat sequences and AT-rich sequences, which are involved in the regulation of the replication and transcription of the mitogenome, were observed in the control region. Phylogenetic analysis revealed that Conoidea is divided into two separate clades with high nodal support. Positive selection analysis revealed evidence of adaptive changes in the mitogenomes of deep-sea conoidean gastropods. Eight residues located in atp6, cox1, cytb, nad1, nad4, and nad5 were determined to have undergone positive selection. This study explores the adaptive evolution of deep-sea conoidean gastropods and provides valuable clues at the mitochondrial level regarding the exceptional adaptive ability of organisms in deep-sea environments.

The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers

The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.

Mitochondrial Short-Term Plastic Responses and Long-Term Evolutionary Dynamics in Animal Species

How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived noncoding RNAs, micropeptides, mtDNA mutations, and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.

Phylogenetic Relationships and Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes

Mitochondrial genomes (mitogenomes) are an excellent source of information for phylogenetic and evolutionary studies, but their application in marine invertebrates is limited. In the present study, we utilized mitogenomes to elucidate the phylogeny and environmental adaptation in deep-sea mussels (Mytilidae: Bathymodiolinae). We sequenced and assembled seven bathymodioline mitogenomes. A phylogenetic analysis integrating the seven newly assembled and six previously reported bathymodioline mitogenomes revealed that these bathymodiolines are divided into three well-supported clades represented by five Gigantidas species, six Bathymodiolus species, and two "Bathymodiolus" species, respectively. A Common interval Rearrangement Explorer (CREx) analysis revealed a gene order rearrangement in bathymodiolines that is distinct from that in other shallow-water mytilids. The CREx analysis also suggested that reversal, transposition, and tandem duplications with subsequent random gene loss (TDRL) may have been responsible for the evolution of mitochondrial gene orders in bathymodiolines. Moreover, a comparison of the mitogenomes of shallow-water and deep-sea mussels revealed that the latter lineage has experienced relaxed purifying selection, but 16 residues of the atp6, nad4, nad2, cob, nad5, and cox2 genes have underwent positive selection. Overall, this study provides new insights into the phylogenetic relationships and mitogenomic adaptations of deep-sea mussels.

The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers

Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.

The complete mitochondrial genome of sea cucumber Stichopus monotuberculatus (aspidochirotida: Stichopodidae)

The sea cucumber, Stichopus monotuberculatus, is an economically important holothuroid in China due to its larger body size and valuable nutrition. However, the taxonomic revision studies of Stichopodidae have been one of the most controversial issues in recent years. Moreover, there remain considerable doubts about a complex of cryptic species within S. monotuberculatus. In this study, we report the complete mitochondrial genome of S. monotuberculatus. The mitogenome has 16,274 base pairs (60.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study adds one more available complete mitogenomes of Stichopus and will provide useful genetic information for future evolutionary and taxonomic classification of Stichopodidae.

The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata

At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.

The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids

The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)_nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.

Characterization of the complete mitochondrial genome of a holothurians species: Holothuria hilla (Holothuroidea: Holothuriidae)

Mitochondrial genome sequence is a great potential method to both resolve disputed taxonomic issues and to infer phylogenetic relationships among holothurians. In this study, we present the complete mitochondrial genome of Holothuria hilla which was 15,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The gene content and arrangement were typical for Holothuroidea ground pattern. The overall base composition was 32.43% A, 27.20% T, 24.35% C and 16.02% G, showing a bias toward A + T (59.63%). The maximum-likelihood tree based on the concatenated 13 protein-coding genes revealed the phylogenetic relationships among the Holothuroidea species.

Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis

The complete Holothuria leucospilata mitochondrial genome was determined and analyzed in this work. It had a circular mapping molecular with a total length of 15,904 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analysis showed that H. leucospilata clustered together with Holothuria scabra and Holothuria forskali. The complete mitochondrial genome provided in this work would be used for elucidation of Holothuroidea conservation genetics and evolutionary relationships.