Nuclear 18S rRNA Gene Sequences Research Articles

Pathogenesis of black shell disease and its effects on survival and growth in the noble scallop Chlamys nobilis

The parasitic disease of mollusks has severely affected the aquaculture industries around the world, and the infestation of polydorids in commercially important mollusks is a serious problem in aquaculture. The black shell disease of noble scallop Chlamys nobilis often occurs, however, pathogeneses and effects on this scallop are unknown. In this study, two species, Polydora haswelli and Polydora lingshuiensis, were identified based on both morphological characteristics and nuclear 18S rRNA gene sequences. Slice observation showed that the tissues of black shell diseased scallops are abnormal compared to the healthy scallops, indicating that infestation of Polydora affects scallop tissues' structure. Metabolomic analysis of polydorids showed harmful metabolites (such as Microcystin LW, Cyclolinopeptides, and Neurosporaxanthin) were significantly higher than these beneficial metabolites (such as Lablabsaponin I, Notoginsenoside E, Taxoprexin, and Candicidin), suggesting these metabolites may cause detrimental effects on hosts. Pathway enrichment analysis of DEGs indicated metabolic pathways (such as amino acid and fatty acid metabolic pathways) and immune-related pathways (such as vibrio, pathogenic, and virus infection pathways) were significantly enriched, which may influence the nutritional quality and immunocompetence. More importantly, the black shell disease can cause high mortality and slow growth in the scallop. This study is the first investigation on the pathogenesis of black shell disease and its effects on survival and growth in the scallop, which is useful for controlling the Polydora infestation in scallop aquaculture.

Occurrence of an unidentified harrimaniid acorn worm in the genus Stereobalanus (Hemichordata: Enteropneusta) from the Japan Trench hadal zone

A number of soft fragments of uncertain identity, mostly taking a form of a disk or button, were found among trawled material from the hadal zone (7426–7654 m in depth) in the Japan Trench during the cruise KH-22-8 of the R/V Hakuho-maru in October 2022. These enigmatic ‘disks’ subsequently turned out to be the proboscides of enteropneusts severed from the collar. A molecular phylogenetic analysis based on the mitochondrial 16S rRNA and nuclear 18S rRNA gene sequences determined from one of the fragments along with others available in public databases indicated that the species in question was sister to the harrimaniid enteropneust Stereobalanus canadensis (Spengel, 1893). Some morphological features of the fragments—the proboscis longitudinal musculature arranged in radial plates, the four tubular ovaries, and the absence of synapticula on the gill bars—support that the Japan Trench species would belong to Stereobalanus Spengel, 1902. This study represents the deepest record of Stereobalanus and the first report of enteropneusts from the Japan Trench hadal zone, albeit identified to the genus level. While the species is putatively undescribed, a formal taxonomic description should await intact specimens in future studies.

Mitogenomics and the Phylogeny of Mantis Shrimps (Crustacea: Stomatopoda)

Stomatopoda, commonly known as mantis shrimps, are notable for their enlarged second maxillipeds encompassing the raptorial claw. The form of the claw can be used to divide them into two basic groups: smashers and spearers. Previous phylogenetic studies of Stomatopoda have focused on morphology or a few genes, though there have been whole mitochondrial genomes published for 15 members of Stomatopoda. However, the sampling has been somewhat limited with key taxa not included. Here, nine additional stomatopod mitochondrial genomes were generated and combined with the other available mitogenomes for a phylogenetic analysis. We used the 13 protein coding genes, as well as 12S rRNA, 16S rRNA genes, and included nuclear 18S rRNA gene sequences. Different rooting options were used for the analyses: (1) single and multiple outgroups from various eumalocostracan relatives and (2) a stomatopod-only dataset, with Hemisquilla californiensis used to root the topologies, based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The eumalocostracan-rooted analyses all showed H. californiensis nested within Stomatopoda, raising doubts as to previous hypotheses as to its placement. Allowing for the rooting difference, the H. californiensis outgroup datasets had the same tree topology as the eumalocostracan outgroup datasets with slight variation at poorly supported nodes. Of the major taxonomic groupings sampled to date, Squilloidea was generally found to be monophyletic while Gonodactyloidea was not. The position of H. californiensis was found inside its superfamily, Gonodactyloidea, and grouped in a weakly supported clade containing Odontodactylus havanensis and Lysiosquillina maculata for the eumalocostracan-rooted datasets. An ancestral state reconstruction was performed on the raptorial claw form and provides support that spearing is the ancestral state for extant Stomatopoda, with smashing evolving subsequently one or more times.

Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)

Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of ‘taxonomics’. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.

Morphology and molecular analysis of the 18S rRNA gene of oyster shell borers, Polydora species (Polychaeta: Spionidae), from Japan and Australia

Nuclear 18S rRNA gene sequences of oyster shell borers, Polydora websteri, P. calcarea and P. haswelli (Polychaeta: Spionidae), were determined for the first time. A wide range of morphological variation, particularly with regard to pigmentation, is observed among these three species. This variation was characterized at the species level. Black pigmentation pattern on the palps is suggested to be a key characteristic for species determination. Polydora websteri and P. haswelli were sister species. This is the first record of P. calcarea from Japan and Australia and P. haswelli from Japan.

The nuclear 18S ribosomal RNA gene as a source of phylogenetic information in the genus Taenia

Most species of the genus Taenia are of considerable medical and veterinary significance. In this study, complete nuclear 18S rRNA gene sequences were obtained from seven members of genus Taenia [Taenia multiceps, Taenia saginata, Taenia asiatica, Taenia solium, Taenia pisiformis, Taenia hydatigena, and Taenia taeniaeformis] and a phylogeny inferred using these sequences. Most of the variable sites fall within the variable regions, V1-V5. We show that sequences from the nuclear 18S ribosomal RNA gene have considerable promise as sources of phylogenetic information within the genus Taenia. Furthermore, given that almost all the variable sites lie within defined variable portions of that gene, it will be appropriate and economical to sequence only those regions for additional species of Taenia.

Morphological and molecular sequence analysis of the harmful shell boring species of Polydora (Polychaeta: Spionidae) from Japan and Australia

Accurate species identification is required to trace, monitor and limit the distribution of harmful shell boring species of the genus Polydora, which have been transported worldwide accompanying commercially important mollusk species. Morphological identification of species in the polydorid complex is difficult because of close similarities, therefore, nuclear 18S rRNA gene sequences were used for the first time to distinguish among the three serious aquaculture pests Polydora brevipalpa, Polydora uncinata, and Polydora aura, from Japan and Australia. The analysis revealed new intraspecific pigmentation variation and confirmed that P. uncinata and P. aura are closely related, possessing special notochaetae on the posterior chaetigers, while P. brevipalpa is a sister taxon to these two species. Polydora brevipalpa and P. uncinata share characteristic black-bar pigmentation on their palps, but they apparently are not part of the same clade.

Authentication of Coscinium fenestratum among the Other Menispermaceae Plants Prescribed in Thai Folk Medicines

In Ayurveda and Thai traditional medicines, material from Coscinium fenestratum is commonly prescribed as active ingredients with diverse therapeutic purposes. However, C. fenestratum is also a seriously endangered medicinal liana. Thus, its crude material is very rare and is being substituted with substances from Arcangelisia flava or Fibraurea tinctoria (Menispermaceae), which have high morphological similarity. In this current study, nuclear 18S ribosomal RNA (rRNA) gene and nuclear ribosomal DNA internal transcribed spacer (ITS) gene sequences with the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique were exploited to identify these three species. The nuclear 18S rRNA gene sequences of C. fenestratum, A. flava, and F. tinctoria consisted of 1809, 1805, and 1809 base pairs (bps), respectively, while their ITS gene regions were 694, 622, and 631 bps in length, respectively. The 18S rRNA gene of C. fenestratum digested with SmaI restriction enzyme displayed the electrophoresis profile of 729 and 790 bps; for A. flava and F. tinctoria, the digested products showed fragments of 1519 bps. Although the ITS gene regions of A. flava and F. tinctoria had unrecognized sequences with SalI, the SalI-digested ITS of C. fenestratum exhibited fragments of approximately 599 bp. Thus, the 18S rRNA gene and ITS gene sequences with PCR-RFLPs were proven to be powerful molecular markers for identifying C. fenestratum and distinguishing it from the other two Menispermaceae plants.

Molecular systematics of Eumolpinae and the relationships with Spilopyrinae (Coleoptera, Chrysomelidae)

The 3400 species of Eumolpinae constitute one of the largest subfamilies of leaf beetles (Chrysomelidae). Their systematics is still largely based on late 19th century monographs and remains highly unsatisfactory. Only recently, some plesiomorphic lineages have been split out as separate subfamilies, including the southern hemisphere Spilopyrinae and the ambiguously placed Synetinae. Here we provide insight into the internal systematics of the Eumolpinae based on molecular phylogenetic analyses of three ribosomal genes, including partial mitochondrial 16S and nuclear 28S and complete nuclear 18S rRNA gene sequences. Sixteen morphological characters considered important in the higher-level systematics of Eumolpinae were also included in a combined analysis with the molecular characters. All phylogenetic analyses were performed using parsimony by optimizing length variation directly on the tree, as implemented in the POY software. The data support the monophyly of the Spilopyrinae outside the clade including all sampled Eumolpinae, corroborating their treatment as a separate subfamily within the Chrysomelidae. The systematic placement of the Synetinae remains ambiguous but consistent with considering it a different subfamily as well, since the phylogenetic analyses using all the available evidence show the representative sequence of the subfamily also unrelated to the Eumolpinae. The Megascelini, traditionally considered a separate subfamily, falls within the Eumolpinae. Several recognized taxonomic groupings within Eumolpinae, including the tribes Adoxini or Typophorini, are not confirmed by molecular data; others like Eumolpini seem well supported. Among the morphological characters analyzed, the presence of a characteristic groove on the pygidium (a synapomorphy of the Eumolpini) and the shape of tarsal claws (simple, appendiculate or bifid) stand out as potentially useful characters for taxonomic classification in the Eumolpinae.

Phylogenetic relationship in the genus Panax: inferred from chloroplast trnK gene and nuclear 18S rRNA gene sequences.

Chloroplast trnK gene and nuclear 18S rRNA gene sequences of 13 Panax taxa, collected mainly from Sino-Japanese floristic region, were investigated in order to construct phylogenetic relationship and to assist taxonomic delimitation within this genus. The length of trnK gene sequence varied from 2537 bp to 2573 bp according to the taxa, whereas matK gene sequences, embedded in the intron of trnK gene, were of 1512 bp in all taxa. Species-specific trnK/ matK sequence provided much insight into phylogeny and taxonomy of this genus. 18S rRNA gene sequences were of 1808 or 1809 bps in length, only 9 types of 18S rRNA sequences were observed among 13 taxa. Parsimony and neighbor-joining analyses of the combined data sets of trnK-18S rRNA gene sequences yielded a well-resolved phylogeny within genus Panax, where three main clades were indicated. P. pseudoginseng and P. stipuleanatus formed a sister group located at a basal position in the phylogenetic tree, which suggested the relatively primitive position of these two species. Monophyly of P. ginseng, P. japonicus (Japan) and P. quinquefolius, which are distributed in northern parts of Asia or America, was well supported (Northern Clade). The remaining taxa distributed in southern parts of Asia formed a relatively large clade (Southern Clade). The taxonomic debated taxa traditionally treated as subspecies or varieties of P. japonicus or P. pseudoginseng showed various nucleotide sequences, but all fell into one cluster. It might suggest these taxa are differentiated from a common ancestor and are in a period of high variation, which is revealed not only on morphological appearance, but also on molecular divergence. By comparing trnK and 18S rRNA gene sequences among 13 Panax taxa, a set of valuable molecular evidences for identification of Ginseng drugs was obtained.

Phylogenetic Analysis of the Mischococcales, Tribonematales, and Vaucheriales (Xanthophyceae) Inferred from 18S rRNA Gene Sequences

AbstractThe Xanthophyceae have traditionally been classified using a phenetic classification system based upon vegetative cell structure. Species belonging to the class are placed in one of six orders corresponding to amoeboid, coccoid, filamentous, flagellate, palmelloid, or siphonous organization. Nuclear 18S rRNA gene sequences were determined for 29 species and aligned with 10 previously determined sequences. Parsimony and maximum likelihood trees inferred from these data imply that the orders Mischococcales (coccoid), Tribonematales (filamentous), and Vaucheriales (siphonous) are not monophyletic. The majority of species are divided between two clades defined by the presence or absence of a bipartite cell wall. Also, several families, particularly those placed in the Mischococcales, are resolved as polyphyletic. Results indicate that coccoid and filamentous life forms may have arisen independently at least three times, and some coccoid and filamentous life forms are resolved as closely related. For example, Heterococcus (filamentous) is more closely related to Mischococcus and Pseudopleurochloris (coccoid) than it is to other members of the Tribonematales. Our data strongly support the contention that Bumilleriopsis and Pseudobumilleriopsis are congeneric with Bumilleria. The siphonous xanthophytes including Asterosiphon, Botrydium, and Vaucheria probably do not form a monophyletic group although robust bootstrap support for this conclusion is low. Our results indicate that the generic, familial, and ordinal classification of the Xanthophyceae requires major revision.

PHYLOGENETIC RELATIONSHIPS WITHIN CLADOPHORALES (ULVOPHYCEAE, CHLOROPHYTA) INFERRED FROM 18S rRNA GENE SEQUENCES, WITH SPECIAL REFERENCE TOAEGAGROPILA LINNAEI 1

The phylogenetic position of a freshwater green alga,Aegagropila linnaei(Cladophorales, Ulvophyceae), was investigated using nuclear 18S rRNA gene sequences. This alga has usually been calledCladophora aegagropila(L.) Rabenhorst orCladophora sauteri(Nees ex Kütz.) Kütz. Based on morphology, it was formerly classified into the sectionAegagropilaor into the subgenusAegagropila, together with several marine species of the genusCladophora.This classification is not supported by the present phylogenetic analyses in which two very distinct Cladophorales clades are recognized.Aegagropila linnaeigroups together in a well‐supported clade withCladophorasp.,Pithophorasp.,Chaetomorpha okamurae,Arnoldiella conchophila,Wittrockiella lyallii, andCladophora conchopheria. Aegagropila linnaeiand its closely related species share some ultrastructural and biochemical characteristics, like pyrenoid structure, carotenoid composition, and cell wall composition. Freshwater species, included in the analysis, were located in two distantly related lineages, indicating that adaptation from a marine to a freshwater habitat has happened at least twice independently in the Cladophorales.

MOLECULAR SYSTEMATICS OF THE XANTHOPHYCEAE

Species belonging to the Xanthophyceae have traditionally been classified in six (or seven) orders corresponding to amoeboid, coccoid, filamentous, monadoid, palmelloid and siphonous lines of descent. We have determined plastid rbcL and nuclear 18S rRNA gene sequences for selected coccoid, filamentous and siphonous species. Phylogenetic trees inferred from these data indicate that the orders Mischococcales (coccoid) and Tribonematales (filamentous) are not monophyletic. Instead, our results indicate that coccoid and filamentous life forms have arisen independently in different xanthophyte lineages. Some coccoid and filamentous species are resolved as close allies. For example, in our analyses coccoid and filamentous species possessing bipartite cell walls (e.g., Bumilleria, Ophiocytium, Tribonema, Xanthonema) form a distinct and previously unrecognized lineage within the class. The phylogenetic positions of Asterosiphon, Botrydium and Vaucheria are not robustly resolved, but our data suggest that these siphonous xanthophytes probably do not form a monophyletic group. Our results imply that Vaucheria is only distantly related to other xanthophytes we have examined. Nucleotide sequence divergence values among Vaucheria species were found to be equal to, or greater than, those observed between other xanthophyte species that are classified in different families or orders. Furthermore, our trees do not always support the infrageneric system of classification for Vaucheria species, which is based primarily upon antheridial features.