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opencc-zeroJun 2022View details →

Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

opencc-zeroOct 2019View details →

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.

opencc-zeroDec 2018View details →

Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes

[No abstract entered]

opencc-zeroDec 2013View details →

Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.

opencc-by-4.0Jul 2022View details →

Fast Intratumor Heterogeneity Inference from Single-Cell Sequencing Data (simulated data - Extended Data Figures)

This data repository contains simulated data used for benchmarking HUNTRESS against the existing alternative tools. Results of the benchmarking are shown in Extended Data Figures 1-10 of the paper "Fast Intratumor Heterogeneity Inference from Single-Cell Sequencing Data" (to appear in Nature Computational Science).

opencc-by-4.0Jul 2022View details →

Supplementary Data for "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" in G-Cubed.

Supplementary data tables for Ma et al. (2022) associated with the paper entitled "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" published in G-Cubed.

opencc-zeroAug 2022View details →

Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

This study aimed to reveal the evolutionary timescale and processes underlying the diversity of Rubus in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, R. chamaemorus, R. pedatus, R. vernus, R. pseudojaponicus, and R. ikenoensis, were found to belong to anciently diverged lineages; in particular, R. ikenoensis formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. Malachobatus, Chamaebatus, and sects. Pungentes, Idaeanthi, and Parvifolii (subg. Idaeobatus), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, R. sieboldii has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. Microphylli, Corchorifolii, Peltati, and Rosifolii (subg. Idaeobatus), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, R. sumatranus, R. peltatus, R. corchorifolius, and R. chingii, was incongruent among gene trees. At the lower taxonomic levels, R. illecebrosus, R. grayanus, and the thornless species of sect. Microphylli showed earlier divergence.

opencc-zeroAug 2022View details →

The cDNA sequence data of hox genes in Daphnia similoides sinensis

Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of Microcystis aeruginosa on Hox gene expression in the mothers and offspring of Daphnia similoides sinensis were investigated using a mixed diet of M. aeruginosa and Scenedesmus obliquus in two clones. The 14 Hox genes sequence were identified in D. similoides sinensisare through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).

FIGURE 22 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 22. Piribelba piriformis (Mihelčič, 1964), paralectotypes (originally syntypes of author). A—solenidion φ1; B— setation of genu III (GeIII), genu and tibia IV (GeIII, TiIV); C—aggenital seta and genital setae, lateral view; D—details of selected setae (all in same scale); E—details of leg setation of another specimen, genu III and IV (GeIII, GeIV), tibia and proximal part of tarsus I (TiI, TsI); F—deutonymph in lateral view (dashed area represents crack in medium where observation is more difficult). Scale bar 100 μm.

FIGURE 29 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 29. Piribelba piriformis (Mihelčič, 1964), adult specimens from Slovakia (A–E: Dreveník, F–G: Sivec). A—dorsal view of the body; B—seta le; C—general view of the body with carried load of debris on notogaster, lateral view; D—legs I–III in lateral view, E—leg IV in lateral view; F—form "lanceata", lateral view; G—form "lanceata", detail of seta d of femur IV.

FIGURE 19 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 19. Piribelba rossica (Bulanova-Zachvatkina, 1957), nymphs from Kemerovo region, light microscope images: A, B—tritonymph, apodemes III at different focus of the microscope; C, D—tritonymph, apodemes II at different focus of the microscope; E—tritonymph, part of prodorsum with lamellar seta; F—deutonymph, genu IV; G—deutonymph, part of tibia IV. Scale bar 50 μm.

FIGURE 26 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 26. Piribelba piriformis (Mihelčič, 1964), adult. Specimen from Austria (Dörfertal): A—dorsal view; B—ventral view; C—seta le in different aspects (left: dorsal to dorsolateral view, right: dorsomedial view); D—bothridial complex. Specimen from Slovakia (Sivec), form "lanceata": E—dorsal view, F—ventral view, G—anal and genital shields; H—seta of ventral and dorsal parts of the body. Scale bars 100 μm (A, B, E, F), 50 μm (D, G, H).

FIGURE 16 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 16. Piribelba rossica (Bulanova-Zachvatkina, 1957), tritonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.

FIGURE 15 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 15. Piribelba rossica (Bulanova-Zachvatkina, 1957), deutonymph from Kemerovo region: A—leg I, right, antiaxial view; B—leg II, right, antiaxial view; C—leg III, right, antiaxial view; D—leg IV, right, antiaxial view. Scale bar 100 μm.

FIGURE 14 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 14. Piribelba rossica (Bulanova-Zachvatkina, 1957), deutonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.

FIGURE 9 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 9. Piribelba rossica (Bulanova-Zachvatkina, 1957), adult from Novosibirsk (A–E) and Tuva (F–K) regions (from Bulanova-Zachvatkina collection), light microscope images: A, F—slides from the collection with type specimen; B—epimeral III–IV and anogenital plates, ventral view; C, D, I–K—notogastral setae; E—femur, genu and tibia I, antiaxial view; G— prodorsum, part, dorsal view; H—distal part of bothridial setae. Scale bars 100 μm (B, G), 50 μm (D–C, H–K).

FIGURE 11 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 11. Piribelba rossica (Bulanova-Zachvatkina, 1957), larva from Kemerovo region: A—leg I, left, antiaxial view; B—tarsus I, left, dorsal view; C—leg II, left, antiaxial view; D—leg IV, left, antiaxial view; E—genu IV, right, dorsal view. Scale bar 100 μm.

FIGURE 28 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 28. Piribelba piriformis (Mihelčič, 1964), adult specimen from Austria (Dörfertal). A —dorsal view; B—ventral view, C—lateral view, D—rostrum and mouthparts in lateral view; E—seta le in dorsal view; F—leg IV, G—detail of femur and genu IV; H—detail of tibia III and IV; I—detail of femur and genu I; J—anterior genital setae in lateral view.

FIGURE 12 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 12. Piribelba rossica (Bulanova-Zachvatkina, 1957), protonymph from Kemerovo region: A—dorsal view (legs only partly drawn); B—ventral view (gnathosoma not shown, legs only partly drawn), C—lateral view (gnathosoma and legs only partly drawn). Scale bar 100 μm.

FIGURE 8 in Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data

FIGURE 8. Piribelba rossica (Bulanova-Zachvatkina, 1957), adult from Kemerovo region, light microscope images: A–F— notogastral setae; G–J—lamellar setae (in various specimens); H—lateral view of the body. Arrow points to distal spines. Scale bars 100 μm (H), 50 μm (A–J).