Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench

Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes

To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level.

Comparative Analysis of the Mitochondrial Genome of Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae) From a Depth of 9,462 m at the Mariana Trench

The hadal zone, which represents the deepest marine habitat on Earth (6,000–11,000 m), is a harsh environment mainly characterized by extremely high hydrostatic pressure, and this habitat is believed to have a high degree of endemism. The deep-sea anemone family Galatheanthemidae comprises two valid species exclusively from the hadal; however, no other information about this family is currently available. In the present study, a sea anemone was collected from a depth of 9,462 m at the Mariana Trench and was defined as Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae). The mitochondrial genome of Galatheanthemum sp. MT-2020 was circular, was 16,633 bp in length, and contained two ribosomal RNA genes, 13 protein-coding genes and two transfer RNA genes. The order of the genes of Galatheanthemum sp. MT-2020 was identical to that of the majority of the species of the order Actiniaria. The value of the AT-skew was the lowest in the whole mitochondrial genome, with a positive GC skew value for the atp8 gene, while other species, except Antholoba achates, had the negative values of the GC skew. Galatheanthemum sp. MT-2020 was clustered with another abyssal species, Paraphelliactis xishaensis, in the phylogenetic tree, and these species diverged in the early Jurassic approximately 200 Mya from the shallow-sea species. The usage ratio of valine, which is one of the five amino acids with the strongest barophilic properties, in the mitochondrial genomes of the two abyssal species was significantly higher than that in other species with habitats above the depth of 3,000 m. The ω (dN/dS) ratio of the genomes was 2.45-fold higher than that of the shallow-sea species, indicating a slower evolutionary rate. Overall, the present study is the first to provide a complete mitogenome of sea anemones from the hadal and reveal some characteristics that may be associated with adaptation to an extreme environment.

Trace Elemental Analysis of the Exoskeleton, Leg Muscle, and Gut of Three Hadal Amphipods

Hadal trenches are the deepest areas worldwide. Amphipods are considered a key factor in hadal ecosystems because of their important impacts on the hadal environment. Amphipods have benthic habits, and therefore, serve as good metal biomonitors. However, little is known about the hadal amphipod metal accumulations. In the present study, Alicella gigantea, Hirondellea gigas, and Scopelocheirus schellenbergi were sampled from the New Britain Trench (8824m, 7.02S 149.16E), Mariana Trench (10,839m, 11.38N 142.42E), and Marceau Trench (6690m, 1.42N 148.74E) in the West Pacific Ocean, respectively. The elemental concentrations of the three hadal amphipods were subsequently investigated. Nine trace elements (V, Cr, Mn, Co, Ni, Se, Mo, Ag, and Cd) of three tissues (exoskeleton, leg muscle, and gut) of the hadal amphipods were detected by using inductively coupled plasma mass spectrometry (ICP-MS) method. The concentrations of Cr, Cd, and Mn were comparably higher among those nine examined elements. The greatest accumulations of the elements Cr, Ag, and V in the exoskeleton and leg muscle were observed in H. gigas, and elements Mn, Co, and Se showed the highest accumulations in the gut in H. gigas among the three hadal amphipods. In addition, comparisons of the leg muscle trace element accumulation between the hadal amphipods and non-abyssal and shallow water decapoda and amphipoda species showed that the hadal amphipods possessed comparably higher concentrations of the trace elements Cd, Co, Mo, Ag, and V. This finding suggested a bottom-up effect of food availability and indicated the effects of human activities within the hadal environments. This study reveals the trace element bio-accumulation of three hadal amphipods, and suggests that deep-sea amphipods are potential indicator species for trace element bioavailability in the deep-sea environment.

Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.

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.

Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

Exceptional Enlargement of the Mitochondrial Genome Results from Distinct Causes in Different Rain Frogs (Anura: Brevicipitidae: Breviceps)

The mitochondrial (mt) genome of the bushveld rain frog (Breviceps adspersus, Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions. To investigate the evolutionary lineage, timing, and process of mt genome enlargement, we sequenced the complete mtDNAs of two congeneric rain frogs, B. mossambicus and B. poweri. The mt genomic organization, gene content, and gene arrangements of these two rain frogs are very similar to each other but differ from those of B. adspersus. The B. mossambicus mt genome (22.5 kbp) does not differ significantly from that of most other afrobatrachians. In contrast, the B. poweri mtDNA (28.1 kbp) is considerably larger: currently the second largest among vertebrates, after B. adspersus. The main causes of genome enlargement differ among Breviceps species. Unusual elongation (12.5 kbp) of the control region (CR), a single major noncoding region of the vertebrate mt genome, is responsible for the extremely large mt genome in B. poweri. Based on the current Breviceps phylogeny and estimated divergence age, it can be concluded that the genome enlargements occurred independently in each species lineage within relatively short periods. Furthermore, a high nucleotide substitution rate and relaxation of selective pressures, which are considered to be involved in changes in genome size, were also detected in afrobatrachian lineages. Our results suggest that these factors were not direct causes but may have indirectly affected mt genome enlargements in Breviceps.

The complete mitochondrial genome of the deep-sea amphipod Eurythenes magellanicus (Crustacea: Amphipoda: Lysianassidae)

The complete mitochondrial genome of the deep sea amphipod Eurythenes magellanicus was determined in this paper. This molecular was 14,988 bp in length, and contained the typical 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one control region (CR). The gene order of E. magellanicus was identical to that from E. maldoror, a deep sea amphipod inhabiting in a deeper habitat than E. magellanicus. A maximum-likelihood tree based on the 13 PCGs from 25 amphipods indicated that E. magellanicus and E. maldoror were closely related and the origin of deep sea amphipods was not monophyletic.

The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters

Alicella gigantea (Alicelloidae) is a scavenger with the largest body size among amphipods. It is a participant in the foodweb of deepsea ecosystem and distributed with vast bathymetric and geographic ranges. In this study, the mitochondrial genome of A. gigantea was completely assembled and characterized. The complete sequence has a total length of 16,851 bp, comprising the usual eukaryotic components, with 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 2 noncoding control regions (CRs). The gene rearrangement and reverse nucleotide strand bias of its mitochondrial genome are similar to those observed in the deepsea amphipod Eurythenes maldoror (Eurytheneidae), but different from the characters of Halice sp. MT-2017 (Dexaminoidea), an inhabitant of a deeper environment. Phylogenetic analysis indicates that A. gigantea occupies the basal branch of deepsea species-E. maldoror and Hirondellea gigas. This phylogeny supports the hypothesis that the evolution of hadal amphipods has undergone a transition from the abyssal depth. Compared to 41 available shallow water equivalents, the four accessible mitochondrial genomes from the deep sea, including the one produced in this study, show significantly fewer charged amino acids in the 13 PCGs, which suggests an adaption to the deepsea environment.