The complete mitochondrial genomes of two octopods Cistopus chinensis and Cistopus taiwanicus: revealing the phylogenetic position of the genus Cistopus within the order Octopoda

Genome skimming elucidates the evolutionary history of Octopoda

Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.

Morphological Description and Phylogenetic Analyses of a New Species of Callistoctopus (Cephalopoda, Octopodidae) from China

A new octopus species, Callistoctopus tenuipes sp. nov., was formally described from the southeastern coastal waters of China using morphological description and molecular analysis methods. C. tenuipes sp. nov. is a small- to moderate-sized octopus, which is characterized by very narrow and long arms. Although it was previously misidentified as the juvenile of Octopus minor (Sasaki, 1920), it can be recognised by spots, gill lamellae count, funnel organ shape, enlarged suckers, and ligula shape. C. tenuipes sp. nov. differs from the small-sized octopus Callistoctopus xiaohongxu, mainly in the gill lamellae count, funnel organ shape, and arm-length index. In the molecular analysis, sequences obtained from the cytochrome c-oxidase subunit I (COI) gene of eight specimens were 590 bp in length. The pairwise Kimura 2-parameter (K2P) genetic distances between Octopodidae species ranged from 8.58 to 23.79% based on the COI gene. The phylogenetic analyses suggested that C. tenuipes sp. nov. belonged to the Callistoctopus clade and may have a close affinity with C. xiaohongxu and O. minor. Moreover, three species delimitation methods all strongly supported C. tenuipes as a separate species.

Morphological description and mitochondrial DNA-based phylogenetic placement of a new species of Callistoctopus Taki, 1964 (Cephalopoda, Octopodidae) from the southeast waters of China

In this study, we described a new species of octopus and named it Callistoctopusxiaohongxu sp. nov. based on nine specimens captured in the waters of southeast China. Callistoctopusxiaohongxu sp. nov. is a small to moderate-sized octopus. The most characteristic and defining morphological features are the reddish-orange to reddish-brown skin, gills with 8 or 9 lamellae per demibranch, \∧/-shaped funnel organ, and small suckers. Fragments obtained from the mitochondrial cytochrome c oxidase subunit I (COI) gene of nine specimens were 593 bp in length, and the genetic distance among the specimens of C.xiaohongxu sp. nov. and the other 16 octopods ranged from 11.13 to 21.09%. Topologies resulting from ML and BI analyses of the COI gene showed a highly supported monophyletic clade (bootstrap value [BS] = 94%, posterior probability [PP] = 100%) containing all the specimens identified as C.xiaohongxu sp. nov.

The full mitochondrial genome sequence of the greater argonaut Argonauta argo (Cephalopoda, Argonautoidea) and its phylogenetic position in Octopodiformes

The greater argonaut Argonauta argo is a species of the paper nautilus (Argonautidae), which is a family in Octopoda. In this paper, we report its full mitogenome sequence, which was obtained from a specimen collected in the Japan Seas near Oki Island, Shimane Prefecture, in Japan. The sequence was determined using the NGS Illumina HiSeq platform. With its 37 genes, the mitogenome shows a typical metazoan and Octopoda genomic structure, and similar to the mitogenome of the previously reported congener, A. hians. To confirm A. argo phylogenetic position in Octopoda, we conducted maximum likelihood phylogenetic analysis, using a data set including publicly available 17 Octopodiformes, five Decapodiformes, three Nautiloids and two outgroup Conchiferans. The result confirmed the affinity of Argonautidae to Tremoctopus, and the sister group position of this clade against the rest of incirrate Octopods. The mitogenome and phylogeny of A. argo reported here will be useful for future studies involving this enigmatic species, including on the reacquisition of external calcified shell structures in mollusks.

Molluscan mitochondrial genomes break the rules

The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae)

This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.

Characterization of the complete mitochondrial genome of the medical pipefish Doryichthys boaja Bleeker 1850

In the present study, we reported the complete mitochondrial genome of medical pipefish Doryichthys boaja Bleeker 1850. The complete mitochondrial genome of D. boaja was 16,562 bp in length and had a base composition of A (31.10%), C (24.14%), G (14.36%), and T (30.40%). Similar to other Syngnathidae species, it contained a typically conserved structure, including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The 13 protein-coding genes encoded 3800 amino acids in total, most of which used the initiation codon ATG except CO1 gene started with GTG. For the stop codon, 6 genes applied TAA as the stop codon, while the other 7 genes used an incomplete stop codon T or TA. The lengths of 12S rRNA and 16S rRNA were 941 bp and 1671 bp, respectively. The control region of D. boaja ranged from 15,615 bp to 16,562 bp, which was 948 bp in length. The complete mitochondrial genome of D. boaja provided essential and important molecular data for phylogeography and evolutionary analysis of Syngnathidae Family.

Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda)

Octopus minor is an economically important resource commonly found in Chinese coastal waters. The nuclear gene (RD and ODH) approach of investigation has not reported in this species. Rhodopsin (RD) and octopine dehydrogenase (ODH) genes were used to elaborate the genetic structure collected from eight localities ranging from the northern to the southern coast of China. In total, 118 individuals for the RD gene and 108 for the ODH were sequenced. Overall (RD and ODH) genes resulted in high (0.741±0.032; 0.805±0.038) haplotype and low nucleotide (0.01261±0.00165; 0.00747±0.00086) diversity. Molecular variance displayed higher values among the populations and lower values within the population where the fixation index FST denoted 0.880 and 0.584 in RD and ODH genes respectively. The Dongshan population clustered separately in a phylogenetic tree as in the haplotype networking assessment. The current data suggests that the Dongshan population needs separate management.

Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas

Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group's traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.

Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance

Karyotype analysis was carried out on gill cells of three species of octopods using a conventional air-drying method. The karyotype results showed that all the three species have the same diploid chromosome number, 2n=60, but with different karyograms as 2n=38M+6SM+8ST+8T, FN (fundamental number)=104 (Cistopus chinensis Zheng et al., 2012), 2n=42M+6SM+4ST+8T, FN=108 (Octopus minor (Sasaki, 1920)) and 2n=32M+16SM+12T, FN=108 (Amphioctopus fangsiao (d'Orbigny, 1839-1841)). These findings were combined with data from earlier studies to infer the genetic relationships between nine species via cluster analysis using the karyotype evolutionary distance (D_e ) and resemblance-near coefficient (λ). The resulting tree revealed a clear distinction between different families and orders which was substantially consistent with molecular phylogenies. The smallest intraspecific evolutionary distance (D_e =0.2013, 0.2399) and largest resemblance-near coefficient (λ=0.8184, 0.7871) appeared between O. minor and C. chinensis, and Sepia esculenta Hoyle, 1885 and S. lycidas Gray, 1849, respectively, indicating that these species have the closest relationship. The largest evolutionary gap appeared between species with complicated karyotypes and species with simple karyotypes. Cluster analysis of D_e and λ provides information to supplement traditional taxonomy and molecular systematics, and it would serve as an important auxiliary for routine phylogenetic study.

Sequencing and analysis of the complete mitochondrial genome of Hippocampus spinosissimus Weber, 1913 (Gasterosteiformes: Syngnathidae)

abtract The complete mitochondrial genome of the Hedgehog Seahorse (Hippocampus spinosissimus) is 16 530 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene organization of H. spinosissimus was similar to that observed in most vertebrate creatures. All protein-coding genes use the typical initiation codon ATG, except for COX1 that uses GTG. The overall base composition of H. spinosissimus is 32.2% for A, 22.72% for C, 30.19% for T, and 14.89% for G, with a slight AT bias of 62.39%. Hippocampus spinosissimus showed a closer genetic relationship with H. kelloggi according to the phylogenetic analysis.

Complete mitochondrial genome of the great seahorse Hippocampus kelloggi Jordan & Snyder, 1901 (Gasterosteiformes: Syngnathidae)

In this study, the complete mitogenome sequence of great seahorse Hippocampus kelloggi (Gasterosteiformes: Syngnathidae) has been amplified and sequenced employing the polymerase chain reaction-based method. The total length of mitochondrial DNA is 16 536 bp and includes 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of H. kelloggi was similar to that observed in most vertebrate creatures. The overall base composition of H. kelloggi is 32.19% for A, 23.68% for C, 29.30% for T, and 14.82% for G, with a slight AT bias of 61.49%. Phylogenetic analyses based on complete mitochondrial genome sequence showed that H. kelloggi has a close genetic relationship to H. reidi, H. ingens, and H. kuda.

Mitochondrial genomes and comparative analyses of Culex camposi, Culex coronator, Culex usquatus and Culex usquatissimus (Diptera:Culicidae), members of the coronator group

BACKGROUND

The Coronator Group currently encompasses six morphologically similar species (Culex camposi Dyar, Culex coronator Dyar and Knab, Culex covagarciai Forattini, Culex usquatus Dyar, Culex usquatissimus Dyar, and Culex ousqua Dyar). Culex coronator has been incriminated as a potential vector of West Nile Virus (WNV), Saint Louis Encephalitis Virus (SLEV), and Venezuelan Equine Encephalitis Virus (VEEV). The complete mitochondrial genome of Cx. coronator, Cx. usquatus, Cx.usquatissimus, and Cx. camposi was sequenced, annotated, and analyzed to provide genetic information about these species.

RESULTS

The mitochondrial genomes of Cx. coronator, Cx. usquatus, Cx.usquatissimus, and Cx. camposi varied from 15,573 base pairs in Cx. usquatus to 15,576 in Cx. coronator. They contained 37 genes (13 protein-encoding genes, 2 rRNA genes, and 22 tRNA genes) and the AT-rich control region. Comparative analyses of the 37 genes demonstrated the mitochondrial genomes to be composed of variable and conserved genes. Despite the small size, the ATP8, ATP6 plus NADH5 protein-encoding genes were polymorphic, whereas tRNAs and rRNAs were conserved. The control region contained some poly-T stretch. The Bayesian phylogenetic tree corroborated that both the Coronator Group and the Culex pipens complex are monophyletic taxa.

CONCLUSIONS

The mitochondrial genomes of Cx. coronator, Cx. usquatus, Cx. usquatissimus and Cx. camposi share the same gene composition and arrangement features that match to those reported for most Culicidae species. They are composed of the same 37 genes and the AT-rich control region, which contains poly-T stretches that may be involved in the functional role of the mitochondrial genome. Taken together, results of the dN/dS ratios, the sliding window analyses and the Bayesian phylogenetic analyses suggest that ATP6, ATP8 and NADH5 are promising genes to be employed in phylogenetic studies involving species of the Coronator Group, and probably other species groups of the subgenus Culex. Bayesian topology corroborated the morphological hypothesis of the Coronator Group as monophyletic lineage within the subgenus Culex.