The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position

Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing

BACKGROUND

The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system.

METHODS AND RESULTS

We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816 bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time.

CONCLUSIONS

We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.

The complete mitochondrial genome of the sand bubbler crab Scopimera longidactyla Shen 1932 (Decapoda: Dotillidae) and its phylogenetic analysis

The sand bubbler crab, Scopimera longidactyla Shen, 1932 (Arthropoda: Malacostraca: Decapoda: Thoracotremata: Dotillidae), is commonly found along tropical and subtropical sandy shores of China, Korea, and Taiwan. Ecologically, it plays an important role in the productivity of sandy shores through their feeding and burrowing activities. In this study, the first complete mitochondrial genome (mitogenome) of S. longidactyla was analyzed using next-generation sequencer. Its mitogenome, circular in structure, spans 15,965 bp with a GC content of 29.97%, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. Its mitogenome arrangement and composition are identical to its two congeners, S. globosa and S. intermedia. Phylogenetic analysis fully supports for the monophyly of the genus Scopimera and the sister relationship between S. longidactyla and S. globosa. The complete mitogenome of S. longidactyla and its phylogenetic implications will provide valuable insights for further studies in phylogenetic and evolutionary biology.

Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species

Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura.

The analyses of the complete mitochondrial genomes of three crabs revealed novel gene rearrangements and phylogenetic relationships of Brachyura

BACKGROUND

Brachyura crab is the largest branch of Decapoda crustacean. Phylogenetic relationships within Brachyura remain controversial to be investigated. The mitochondrial genome (mitogenome) is an important molecular marker for studying the phylogenetic relationships of Brachyura.

METHODS AND RESULTS

To understand the phylogeny of Brachyura, the three complete mitogenomes from Charybdis annulata, Leptodius exaratus, and Spider crab were sequenced and annotated. Their full length was 15,747, 15,716, and 16,608 bp long, respectively. The first two crabs both contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. However, Spider crab contained 13 PCGs, two rRNA genes, 25 tRNA genes and a control region. The mitogenomes of each of the three crabs exhibited high AT content (67.8%, 69.1%, and 70.8%), with negative AT skews (-0.014, - 0.028, and - 0.017) and GC skews (-0.269, - 0.286, and - 0.341). The gene order of C. annulata was identical to the ancestor of Brachyura. Compared with the ancestor of Brachyura, L. exaratus exhibited the gene rearrangements of Val (V)-rrnS-control region, and Spider crab had the four copies of Lys (K). Phylogenetic analyses indicated that C. annulata belonged to Portunidae family, Portunoidea superfamilies, L. exaratus belonged to Xanthidae family, Xanthoidea superfamilies, and Spider crab belonged to Mithracidae family, Majoidea superfamilies. Phylogenetic analyses showed that the two species (Somanniathelphusa boyangensis and Huananpotamon lichuanense) belonging to the Potamoidea were sister groups to the Thoracotremata, thus supporting the conclusion that Heterotremata is polyphyletic.

CONCLUSION

The results of this study enriched the crab mitogenome database and enabled us to better understand the phylogenetic relationships of Brachyura.

Populations of the Intertidal Crab Macrophthalmus banzai are Not Grouped by Latitude: Taiwan Population is Genetically Closer to the Populations in the Japanese Mainland Than the Ryukyu Islands

Macrophthalmus banzai is an intertidal crab species of Macrophthalmidae inhabiting muddy tidal flats in the northwestern Pacific. A previous study on the population genetic structure of Japanese M. banzai based on the mitochondrial COI gene sequences revealed the presence of two genetically distinguished groups, i.e., the northern group (Honshu, Shikoku, and Kyushu Islands) and the southern group (the Ryukyu Islands). In the present study, we newly determined the COI gene sequences of M. banzai collected from Taiwan and conducted population genetic analyses of these sequences together with Japanese sequences obtained from GenBank to reveal the genetic relationship of this species between Japan and Taiwan. The SAMOVA and pairwise ΦST analysis showed that the Taiwan population is more closely related to the northern group than the southern group. This indicates that the populations of M. banzai are not genetically differentiated by latitude but probably by the pathway of the Kuroshio Current, resulting in the isolation of the population in the Ryukyu Islands. Such a pattern is consistent with the population genetic structure of the fiddler crab Tubuca arcuata shown by a previous study, whereas the pattern differs from those of other intertidal invertebrates. The difference in the larval durations may have influenced the difference in population genetic structures among species. The present study provides a further case of the genetic structure of intertidal species that are not simply regulated by geographic distances.

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

Comparative mitogenomes provide new insights into phylogeny and taxonomy of the subfamily Xenocyprinae (Cypriniformes: Cyprinidae)

Xenocyprinae is a cyprinid subfamily that not only has a discrete geographic distribution but also has a long history dating to the Early Miocene. However, it is controversial whether systematic classification and some species validity of Xenocyprinae exist, as well as its phylogenetic relationships and evolutionary history. In the present study, we first reviewed the description and taxonomic history of Xenocyprinae, and then the complete mitochondrial genome of Distoechodon compressus, an endemic and locally distributed species belonging to Xenocyprinae, was sequenced and annotated. Finally, all the mitogenomes of Xenocyprinae were compared to reconstruct the phylogenetic relationship and estimate the divergence time. The results showed that the mitogenomes are similar in organization and structure with 16618–16630 bp length from 12 mitogenomes of eight species. Phylogenetic analysis confirmed the monology of Xenocyprinae and illustrated three clades within the Xenocyprinae to consist of ambiguous generic classification. Plagiognathops is a valid genus located at the base of the phylogenetic tree. The genus Xenocypris was originally monophyletic, but X. fangi was excluded. Divergence time estimation revealed that the earliest divergence within Xenocyprinae occurred approximately 12.1 Mya when Plagiognathops separated from the primitive Xenocypris. The main two clades (Xenocypris and (Distoechodon + Pseudobrama + X. fangi)) diverged 10.0 Mya. The major divergence of Xenocyprinae species possibly occurred in the Middle to Late Miocene and Late Pliocene, suggesting that speciation and diversifications could be attributed to the Asian monsoon climate. This study clarifies some controversial issues of systematics and provides essential information on the taxonomy and phylogeny of the subfamily Xenocyprinae.

Molecular phylogeny of Thoracotremata crabs (Decapoda, Brachyura): toward adopting monophyletic superfamilies, invasion history into terrestrial habitats and multiple origins of symbiosis

The Thoracotremata is a large and successful group of "true" crabs (Decapoda, Brachyura, Eubrachyura) with a great diversity of lifestyles and well-known intertidal representatives. The group represents the largest brachyuran radiation into terrestrial and semi-terrestrial environments and comprises multiple lineages of obligate symbiotic species. In consequence, they exhibit very diverse physiological and morphological adaptations. Our understanding of their evolution is, however, largely obscured by their confused classification. Here, we resolve interfamilial relationships of Thoracotremata, using 10 molecular markers and exemplars from all nominal families in order to reconstruct the pathways of lifestyle transition and to propose a new taxonomy corresponding to phylogenetic relationships. The results confirm the polyphyly of three superfamilies as currently defined (Grapsoidea, Ocypodoidea and Pinnotheroidea). At the family level, Dotillidae, Macrophthalmidae, and Varunidae are not monophyletic. Ancestral state reconstruction analyses and divergent time estimations indicate that the common ancestor of thoracotremes already thrived in intertidal environments in the Late Cretaceous and terrestrialization became a major driver of thoracotreme diversification. Multiple semi-terrestrial and terrestrial lineages originated and radiated in the Early Eocene, coinciding with the global warming event at the Paleocene-Eocene Thermal Maximum (PETM). Secondary invasions into subtidal regions and colonizations of freshwater habitats occurred independently through multiple semi-terrestrial and terrestrial lineages. Obligate symbiosis between thoracotremes and other marine macro-invertebrates evolved at least twice. On the basis of the current molecular phylogenetic hypothesis, it will be necessary in the future to revise and recognize seven monophyletic superfamilies and revisit the morphological character states which define them.

Comparative Mitogenome Analyses of Subgenera and Species Groups in Epeorus (Ephemeroptera: Heptageniidae)

Simple Summary

As one of the most species-rich genera of Ephemeroptera, Epeorus Eaton, 1881, was found to be widely distributed in Holarctic and Oriental regions, and nine subgenera have been reported. Previous phylogenetic studies of Epeorus were mainly focused on morphological characters or several gene fragments. Here, 15 mitogenomes of Epeorus are sequenced and the comparative mitogenome analysis of six subgenera is performed. The gene rearrangement of trnI-trnM-trnQ-NCR-ND2 was first found in the genus. In addition, differences in genetic composition and codon usage between the species with this kind of rearrangement and other Epeorus species were observed. Phylogenetic analyses show that three subgenera, Proepeorus, Belovius and Iron, are not monophyletic groups, and our results imply that gill structures are not always appropriate for the classification of subgenera in Epeorus.

Abstract

Epeorus Eaton, 1881 is a diverse mayfly genus in Heptageniidae comprising more than 100 species which are further divided into nine subgenera and several species groups. However, the classification and the phylogenetic relationships among them are still uncertain. Here, 15 complete mitochondrial genomes of Epeorus were sequenced and compared together with six available ones of same genus in the NCBI database. Based on morphological classification, the 21 mitogenomes were classified into six subgenera (Proepeorus, Epeorus s.str., Belovius, Iron, Caucasiron and Siniron) and four species groups (G1, G2, montanus and longimanus). Among all analyzed mitogenomes, the gene rearrangement of trnI-trnM-trnQ-NCR-ND2 was first found occurring in three species of group G1, whereas the gene block trnI-trnM-trnQ-trnM-ND2 was observed in all other mitogenomes of Epeorus. Furthermore, the genetic composition and codon usage of species in group G1 were also significantly different from all other Epeorus species, except group longimanus. The intergenic spacer between trnA and trnR, which has the stem-loop secondary structure, occurred in all 21 mitogenomes, and the sequences of stems and loops were conserved within species groups. Furthermore, the phylogenetic analyses strongly support the monophyly of all species groups, although three of six recognized subgenera Proepeorus, Belovius, and Iron, were shown as the non-monophyletic groups.

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.

Molecular phylogenetic assessment of Spirobranchus kraussii-complex (Annelida: Serpulidae) from the Japanese Archipelago

Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex.