Nucleotide Sequence Data Research Articles

A computational screen for alternative genetic codes in over 250,000 genomes.

The genetic code has been proposed to be a 'frozen accident,' but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force that likely helped drive these codons to low frequency and enable their reassignment.

A rare moss Cynodontium suecicum (Rhabdoweisiaceae, Bryophyta) on the Barents Sea coast of the Kola Peninsula: morphological and molecular study

Specimens of the rare species Cynodontium suecicum (Rhabdoweisiaceae, Bryophyta) were collected near Drozdovka Bay on the Barents Sea coast of the Kola Peninsula (Russia) in 2016. They were compared with samples of C. suecicum from the Teriberka area (also the coast of the Barents Sea) gathered in 1977 by R. N. Schljakov. The morphological features of both groups of samples were studied, and nucleotide sequence data for ITS1-2 nrDNA and trnL-F cpDNA were obtained. Molecular analysis suggested C. suecicum as a hybrid that inherited cytoplasmic DNA from C. tenellum and nuclear DNA from Kiaeria blyttii. Taking into account the rather clear morphological delimitation against other species, combined with the stability of genetic characters, we believe that S. suecicum should be retained as a species-level taxon.

Relationship among bats, parasitic bat flies, and associated pathogens in Korea

BackgroundBats are hosts for many ectoparasites and act as reservoirs for several infectious agents, some of which exhibit zoonotic potential. Here, species of bats and bat flies were identified and screened for microorganisms that could be mediated by bat flies.MethodsBat species were identified on the basis of their morphological characteristics. Bat flies associated with bat species were initially morphologically identified and further identified at the genus level by analyzing the cytochrome c oxidase subunit I gene. Different vector-borne pathogens and endosymbionts were screened using PCR to assess all possible relationships among bats, parasitic bat flies, and their associated organisms.ResultsSeventy-four bat flies were collected from 198 bats; 66 of these belonged to Nycteribiidae and eight to Streblidae families. All Streblidae bat flies were hosted by Rhinolophus ferrumequinum, known as the most common Korean bat. Among the 74 tested bat flies, PCR and nucleotide sequencing data showed that 35 (47.3%) and 20 (27.0%) carried Wolbachia and Bartonella bacteria, respectively, whereas tests for Anaplasma, Borrelia, Hepatozoon, Babesia, Theileria, and Coxiella were negative. Phylogenetic analysis revealed that Wolbachia endosymbionts belonged to two different supergroups, A and F. One sequence of Bartonella was identical to that of Bartonella isolated from Taiwanese bats.ConclusionsThe vectorial role of bat flies should be checked by testing the same pathogen and bacterial organisms by collecting blood from host bats. This study is of great interest in the fields of disease ecology and public health owing to the bats’ potential to transmit pathogens to humans and/or livestock.Graphical abstract

Open Access and Data Sharing of Nucleotide Sequence Data

Open access, free access, and the public domain are different concepts. The International Nucleotide Sequence Database Collaboration (INSDC) permanently guarantees free and unrestricted access to nucleotide sequence data for all researchers, irrespective of nationality or affiliation. However, recent virus information is primarily distributed via the restricted-access repository known as the Global Initiative on Sharing Avian Flu Data (GISAID) supported by the World Health Organization. As compensation for the restriction, GISAID needs to meet its initial goal of benefit-sharing among countries and to curb ongoing vaccine diplomacy campaigns.

Hedyotis hamiguitanensis (Rubiaceae: Spermacoceae), a new species from Mt. Hamiguitan, Davao Oriental, Philippines and its systematic position in Hedyotis

Hedyotis hamiguitanensis, from Mt. Hamiguitan, Davao Oriental, Philippines, is described, illustrated, and compared with two similar species, H. whiteheadii and H. schlechteri. This species is distinguished from congeneric Philippine species by its 5–12 cm long, compound, umbellate inflorescences, pendulous flowers, lanceolate to oblanceolate, thick, scabrid leaf blades with revolute margins. Its phylogenetic systematic position within the tribe Spermococeae is determined with a phylogenetic analysis using chloroplast (rps16, petD) and nuclear ribosomal (ITS, ETS) nucleotide sequence data.

Aligning Standards Communities: Sustainable Darwin Core MIxS Interoperability

Biodiversity is increasingly being assessed using omic technologies (e.g. metagenomics or metatranscriptomics); however, the metadata generated by omic investigations is not fully harmonised with that of the broader biodiversity community. There are two major communities developing metadata standards specifications relevant to omic biodiversity data: TDWG, through its Darwin Core (DwC) standard, and the Genomic Standard Consortium (GSC), through its Minimum Information about any (x) Sequence (MIxS) checklists. To prevent these specifications leading to silos between the communities using them (e.g. INSDC: an internationally mandated database collaboration for nucleotide sequencing data [from health, biodiversity, microbiology, etc.] using the MIxS checklists; OBIS and GBIF: global biodiversity data networks using the DwC standard), there is a need to harmonise them at the level of the standards organisations themselves. To this end, we have brought together representatives from these standardisation bodies, along with representatives from established biodiversity data infrastructures, domain experts, data generators, and publishers to develop sustainable interoperability between the two specifications. Together, we have: generated a semantic mapping between the terminology used in each specification, and syntactic mapping of their associated values following the Simple Standard for Sharing Ontology Mappings (SSSOM), and created an example MIxS-DwC extension showing the incorporation of unmapped MIxS terms into a DwC-Archive. generated a semantic mapping between the terminology used in each specification, and syntactic mapping of their associated values following the Simple Standard for Sharing Ontology Mappings (SSSOM), and created an example MIxS-DwC extension showing the incorporation of unmapped MIxS terms into a DwC-Archive. To sustain these mechanisms of interoperability, we have proposed a Memorandum of Understanding between the GSC and TDWG. During our work, we also noted a number of key challenges that currently preclude interoperation between these two specifications. In this talk, we will outline the major steps we took to get here, as well as the future activities we recommend based on our outputs.

Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics.

Onychophora (“velvet worms”) are charismatic soil invertebrates known for their status as a “living fossil,” their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group’s evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.

The complete mitochondrial genome of Indian Cuckoo Cuculus micropterus (Aves: Cuculiformes)

The Indian Cuckoo, Cuculus micropterus, belongs to the family Cuculidae. In this paper, we sequenced and analysized the complete mitochondrial genome of C. micropterus. The complete mitochondrial genome of C. micropterus is 17,541 bp in length, which was submitted to the NCBI database under the accession number MZ048030. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA is 33.2% for A, 24.2% for T, 29.8% for C, and 12.8% for G, with a GC content of 42.6%. In order to explore the molecular phylogenetics evolution of Cuculidae, the nucleotide sequence data of 13 PCGs of C. micropterus and other 11 Cuculiformes were used for the phylogenetic analysis. The result shows that C. micropterus is closely related to Cuculus canorus bakeri. The study contributes to illuminating the taxonomic status of C. micropterus, and may facilitate further investigation of the evolution of Cuculidae.

Epiphyas intrepidasp. nov. (Lepidoptera: Tortricidae): an endemic, not a stowaway, on Lord Howe Island

AbstractThe tortricid moth genusEpiphyasTurner, 1927, comprises 39 described species and is largely confined to the Australian mainland and Tasmania. Lord Howe Island is the only other place where more than oneEpiphyasspecies is found, these beingEpiphyas postvittana(Walker, 1863), a widely polyphagous and widespread horticultural pest commonly known as the ‘light brown apple moth’, and a second species identified by J. D. Bradley asEpiphyas aulacana(Meyrick, 1881). Because Lord Howe Island is on the UNESCO's world heritage register, it is important to distinguish native from exotic insects as a means for uncovering and managing biosecurity threats to the island. To test whetherE. aulacanasensu Bradley is indeed conspecific withE. aulacana‐like moths from the Australian mainland and Tasmania, specimens from all three islands were examined, and nucleotide sequence data obtained and compared from the mitochondrial gene region cytochromecoxidase subunit I (COI) and three nuclear gene regions: isocitrate dehydrogenase (IDH), malate dehydrogenase (MDH), and the carbomoylphosphate synthetase (CPS) domain of the gene known as CAD. The results suggest that the second species is notE. aulacanabut a new species,Epiphyas intrepidasp. nov., which like its larval host plantCassinia tenuifoliaBentham, 1867, is endemic to the island.

Combining molecular datasets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)

AbstractExtant members of the ancient insect order of stoneflies exhibit a disjunct, antitropical distribution, with one major lineage exclusively occurring in the Southern Hemisphere and the other, with few exceptions, on the Northern continents. Here, we address the biogeographic distribution and phylogenetic relationships of stoneflies using a phylogenetic workflow that combines both transcriptomic and Sanger sequence datasets with heterogeneous taxon coverage. We used a dataset comprising 2997 genes derived from the transcriptomes of 30 species and Sanger sequences of seven genes for 498 species. The backbone phylogeny was mainly inferred from the transcriptomic data, whereas the Sanger nucleotide sequence data provided high species density for divergence time estimation and diversification analyses. Our results show that the biogeographic pattern we observe today is primarily more likely shaped by long‐distance over‐land dispersal than by vicariance. We inferred that the ancestors of extant stoneflies originated in the Northern Hemisphere approximately 265 Ma and were presumably restricted to this area due to climatic and geographic boundaries. Our analyses suggest that with the break‐up of Pangaea around 200 Ma and the associated climatic and geographical changes, two groups of stoneflies, the Anarctoperlaria and the Notonemouridae, dispersed to Gondwana and subsequently went extinct on the northern continents. Both groups likely dispersed across Gondwana before its break‐up into the modern continents. At least one member of another group of ‘northern’ stoneflies, the Acroneuriinae, seems to have migrated from North America to South America around 67 Ma. We found four major net diversification rate shifts, indicating rapid radiation patterns that hampered a robust phylogenetic placement of these stonefly groups. Our study provides the first conclusive evolutionary explanation for the unique distribution pattern of stoneflies.

Characterization of the complete mitochondrial genome of Sinocyclocheilus lingyunensis (Cypriniformes: Cyprinidae)

Sinocyclocheilus lingyunensis is endemic to Youjiang River in Guangxi, Southwestern China. In this study, the complete mitochondrial genome of S. lingyunensis was sequenced. It was determined to be 16,572 bases. The overall base composition was 31.9% A, 25.3% T, 26.9% C, 15.9% G with 42.8% GC content. The nucleotide sequence data of 12 heavy-strand protein-coding genes of S. lingyunensis and other 16 Sinocyclocheilus species were used for phylogenetic analyses. Trees constructed using Bayesian inference showed strong support for a topology indicating Sinocyclocheilus species as a monophyletic group.

The First Mitogenomes of the Subfamily Odontiinae (Lepidoptera, Crambidae) and Phylogenetic Analysis of Pyraloidea.

Simple SummaryThe Odontiinae is a small group in the Pyraloidea comprised of 388 species in 88 genera, but externally, these moths are diverse, including heterogeneous maculation and a size range from 9 to 50 mm in total wingspan. The monophyly of Pyraloidea and the two families (Pyralidae and Crambidae) is well supported by phylogenetic analyses based on morphology and molecular data of multiple nuclear genes. However, only a few mito-phylogenetic analyses have been conducted and no mitogenome of Odontiinae species has been reported. Three complete mitogenomes of odontiine species were sequenced and analyzed for the first time herein. The results showed that Odontiinae mitogenomes shared similar genomic characters with other Pyraloidea. The phylogenetic analyses based on 13 PCGs of mitogenomes confirmed the monophyly of Odontiinae and its position within Crambidae.The complete mitochondrial genomes of three species of Odontiinae were newly sequenced: Dausara latiterminalis Yoshiyasu, Heortia vitessoides (Moore), and Pseudonoorda nigropunctalis (Hampson). These circular and double-stranded mitogenomes vary from 15,084 bp to 15,237 bp in size, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A + T-rich region. The nucleotide composition indicated a strong A/T bias. Most PCGs are initiated with an ATN codon and terminated by a codon of TAR. All tRNAs could be folded into the clover-leaf structure with the exception of trnS1 (AGN), in which the dihydrouridine (DHU) arm formed a simple loop, and the motif ‘ATAG’ and ‘ATTTA’ in the A + T-rich region was also founded. The phylogenomic analyses covering Odontiinae + 11 subfamilies of Pyraloidea were conducted. Similar topologies were generated from both Bayesian inference (BI) and maximum likelihood (ML) analyses based on the nucleotide and amino acid sequence data. There was some discrepancy in the sister-group relationship of Odontiinae and Glaphyriinae, and the relationships among the subfamilies in the ‘CAMMSS clade’ of the Crambidae. The results of this study suggest that mitogenomic data are useful for resolving the deep-level relationships of Pyraloidea and the topologies generated from amino acid data might be more realistic and reliable. Moreover, more mitogenomic taxon sampling and larger scale analyses with more genes or a combination of mitogenomic and nuclear genes are needed to reconstruct a comprehensive framework of the pyraloid phylogeny.

Homozygous ITGA3 Missense Mutation in Adults in a Family with Syndromic Epidermolysis Bullosa (ILNEB) without Pulmonary Involvement

Homozygous ITGA3 Missense Mutation in Adults in a Family with Syndromic Epidermolysis Bullosa (ILNEB) without Pulmonary Involvement

CALLIPHORIDAE (REVIEW)

The Calliphoridae family attracts many researchers in the phylogeny of myiasis in this family. Nevertheless, even after more than 50 years of research of the phylogenetic relationships among Calliphoridae subfamilies, the origin of myiasis remains unclear. By studying the peculiarities of the ecology of blue-green meat flies, and their adaptation to various habitats, it was found that the transition to facultative parasitism at the larval stage could occur in several ways, and was accompanied by the formation of viviparity. The larval parasitism of Calliphoridae on birds developed as a tendency of evolution. Larvae of the genus Protocalliphora, began feeding on blood of birds, and larvae of the species of the genus Trypocalliphora feed on the host tissues causing myiasis and the death of chicks. In order to elucidate the problem, we constructed three phylogenetic trees using nucleotide sequence data from cytochrome oxidase subunit one gene (COI), representing a mitochondrial conservative gene, and nuclear 28S subunit of ribosomal RNA gene (28S rRNA) in order to interpret the evolutionary profile of myiasis in the family Calliphoridae. Comparative analysis of the phylogenetic trees shows that the habit of obligatory myiasis originated independently more than five times among different calliphorid taxa in the course of evolutionary history. The inclusion of other myiasis-causing families (Oestridae, Gastrophilidae, and Sarcophagidae) along with fundamental life-history studies that deal with biology, physiology, feeding behavior and host specificity in addition to phylogenetic analysis could provide a more accurate answer to the origin of myiasis

Characterization of the mitochondrial genome of Tinda javana (Macquart, 1838) (Diptera: Stratiomyidae: Pachygastrinae)

We have assembled and annotated the mitochondrial genome of Tinda javana (Macquart, 1838) (a species of soldier fly) in this study. It is 15,495 bp in length, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a large non-coding control region (length: 704 bp). The nucleotide composition of whole mitochondrial genome biases toward A and T (75.5%). Most PCGs use ATN as initiation codon, except for cox1 which starts with CGA. All PCGs end with common termination codon TAA/G. Phylogenetic analyses based on the nucleotide sequence data supported the monophyly of Stratiomyidae and the sister relationship between Pachygastrinae and the clade (Nemotelinae + (Hermetiinae + Sarginae)).

Morphological and molecular evidence support the taxonomic separation of the medically important Neotropical spiders Phoneutria depilata (Strand, 1909) and P. boliviensis (F.O. Pickard-Cambridge, 1897) (Araneae, Ctenidae).

The species of the genus Phoneutria (Ctenidae), also called banana spiders, are considered amongst the most venomous spiders in the world. In this study we revalidate P. depilata (Strand, 1909), which had been synonymized with P. boliviensisis (F.O. Pickard-Cambridge, 1897), using morphological and nucleotide sequence data (COI and ITS-2) together with species delimitation methods. We synonymized Ctenus peregrinoides, Strand, 1910 and Phoneutria colombiana Schmidt, 1956 with P. depilata. Furthermore, we designated Ctenus signativenter Strand, 1910 as a nomen dubium because the exact identity of this species cannot be ascertained with immature specimens, but we note that the type locality suggests that the C. signativenter syntypes belong to P. depilata. We also provide species distribution models for both species of Phoneutria and test hypotheses of niche conservatism under an allopatric speciation model. Our phylogenetic analyses support the monophyly of the genus Phoneutria and recover P. boliviensis and P. depilata as sister species, although with low nodal support. In addition, the tree-based species delimitation methods also supported the separate identities of these two species. Phoneutria boliviensis and P. depilata present allopatric distributions separated by the Andean mountain system. Species distribution models indicate lowland tropical rain forest ecosystems as the most suitable habitat for these two Phoneutria species. In addition, we demonstrate the value of citizen science platforms like iNaturalist in improving species distribution knowledge based on occurrence records. Phoneutria depilata and P. boliviensis present niche conservatism following the expected neutral model of allopatric speciation. The compiled occurrence records and distribution maps for these two species, together with the morphological diagnosis of both species, will help to identify risk areas of accidental bites and assist health professionals to determine the identity of the species involved in bites, especially for P. depilata.

The complete mitochondrial genome of white-tailed mole (Parascaptor leucura)

The white-tailed mole (Parascaptor leucura) belongs to genus Parascaptor, which is a monotypic genus distributed across Southwestern China, Assam (India), Bengal, and Northern Burma, and Laos. In this study, we obtained the complete mitochondrial genome of Parascaptor leucura. The genome is total 16,875 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions, with a base composition of 33.5% A, 26.4% T, 25.7% C, and 14.3% G. The nucleotide sequence data of 13 protein-coding genes of P. leucura and other nine Eulipotyphla species were used to reconstruct a Bayesian phylogenetic tree. The tree shows that P. leucura belongs to subfamily Talpinae and is closely related to Scaptochirus moschatus.

Transcription factor binding site detection using convolutional neural networks with a functional group-based data representation

Transcription factors (TFs) play an essential role in molecular biology by regulating gene expression. The binding sites of TFs can vary by a large amount and the numerous possible binding locations make their detection a challenging issue. Recently, several machine learning approaches using nucleotide sequence data were applied to classify DNA sequences regarding Transcription Factor Binding Sites (TFBS). We propose a novel training strategy without the traditional 1D nucleotide-based DNA sequence representation by instead using a 2D topological matrix of sub-nucleotide chemical functional groups substantially defining the protein binding ability of DNA fragments. We train convolutional neural networks using this novel Functional Group DNA Representation (FGDR) to solve a TFBS classification task. We compare our results with the efficiency of previous nucleotide-based training approaches and show that learning from an FGDR data sequence has several benefits regarding TFBS classification. Moreover, we reason that learning deep neural networks from the FGDR representation produces competitive results while only introducing a pre-processing conversion step. Finally, we show that employing an ensemble of models from the nucleotide and FGDR representations for network training results in higher classification performance than any of the single input approaches.

The molecular profile of Acanthogyrus (Acanthosentis) kashmirensis from the Indian subcontinent.

The purpose of the present study was to provide molecular support for the validity of the morphological description of Acanthosentis kashmirensis Amin, Heckmann, Zargar, 2017 which was originally poorly described as Neoechinorhynchus kashmirensis Fotedar and Dar, 1977 from the Indian subcontinent, and to characterise its molecular identity and phylogenetic relationships. Total DNA was extracted, and the partial region of the small subunit (SSU) 18S rDNA and ITS-rDNA genes were amplified and sequenced. Genetic diversity was calculated and phylogenetic analysis of the nucleotide sequence data was performed. In this study, the molecular profile of this acanthocephalan was generated for the first time. Based on the partial 18S rDNA, interspecific variation between A. kashmirensis with different species of Acanthosentis and were 3.6-10.3% and 22.4-38.2% based on 18S rDNA and ITS-rDNA genes, respectively. We described the phylogenetic relationships of A. kashmirensis compared with other species of the genus and also with members of the family Quadrigyridae. The ITS-rDNA sequences of members of the family Quadrigyridae are more variable than 18S rDNA that can be useful for achieving a proper assessment of biodiversity. Sequence data generation from additional species of Acanthosentis will be needed to reconstruct the phylogenetic relationships of this group of acanthocephalans.

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication.

Simple SummaryHeptageniidae is one of the most abundant and widespread families of mayflies, with more than 600 described species and distributed mainly in the Holoarctic, Oriental, and Afrotropical regions. Previous phylogenetic analyses in this family mainly focused on morphological characters and were restricted to one or several genes. Ten complete mitochondrial genomes from this family are reported here. A conserved intergenic spacer and tRNA gene duplication in Heptageniidae mitogenomes may be regarded as ancient features and provide evidence for the phylogenic analysis within Ephemeroptera.Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.