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opencc-zeroDec 2017View details →

Data from: Delimiting species of marine gastropods (Turridae, Conoidea) using RAD-sequencing in an integrative taxonomy framework

Species delimitation in poorly-known and diverse taxa is usually performed based on monolocus, DNA barcoding-like approaches, while multilocus data are often used to test alternative species hypotheses in well-studied groups. We combined both approaches to delimit species in the Xenuroturris / Iotyrris complex, a group of venomous marine gastropods from the Indo-Pacific. First, COI sequences were analyzed using three methods of species delimitation, ABGD, PTP and GMYC to propose primary species hypotheses (PSH). Second, RAD-seq data were also obtained and an IQ-tree phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-seq data. Alternative species partitions revealed with the COI dataset were also tested using the RAD-seq data and the BFD method. The congruence between the species hypotheses proposed with the mitochondrial gene and the clades in the RAD-seq tree, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the PSH into secondary species hypotheses (SSH). Allopatric PSH defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.

opencc-zeroDec 2014View details →

Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing

Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.

opencc-zeroDec 2014View details →

Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

opencc-zeroDec 2016View details →

Data from: Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum

Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus. IMPORTANCE: The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

opennotspecifiedAug 2014View details →

FIGURE 1 in Studies on Wrightoporia from China 3. Wrightoporia subavellanea sp. nov. based on morphological characters and rDNA sequence data

FIGURE 1. Fresh basidiocarps of Wrightoporia subavellanea (Dai 10826). Scale bar = 1cm.

opencc-zeroSep 2016View details →

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single nucleotide polymorphisms (SNPs), of which 1,590,653 high confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype restricted non-synonymous SNPs that are predicted to impact protein function in genes that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17,228 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.

opencc-zeroDec 2020View details →

Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of DNA sequence data

The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK and wingless) and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI ("barcode" region) and COI ("Pat/Jer" region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all except Notiokasis and Archileistobrius), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. Tribes Notiophilini, Opisthiini, Pelophilini, Nebriini are well supported as monophyletic but relationships among these are not well resolved. Nippononebria is a distinct genus more closely related to Leistus than Nebria. Archastes, Oreonebria, Spelaeonebria, and Eurynebria, previously treated as distinct genera by some authors, are all nested within a monophyletic genus Nebria. Within Nebria, four major clades are recognized: (1) the Oreonebria Series, including eight subgenera arrayed in two subgeneric complexes (the Eonebria and Oreonebria Complexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) the Nebria Series, including ten subgenera arrayed in two subgeneric complexes, the Boreonebria and Nebria Complexes, with the latter further subdivided into three subgeneric subcomplexes (the Nebria, Epinebriola and Eunebria Subcomplexes)); and (4) the Catonebria Series, including seven subgenera arrayed in two subgeneric complexes (the Reductonebria and Catonebria Complexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (Nippononebria, Vancouveria and Archastes) are given revised status and seven are recognized as new synonymies (Nebriorites Jeannel, 1941 and Marggia Huber, 2014 = Oreonebria Daniel, 1903; Pseudonebriola Ledoux and Roux, 1989 = Boreonebria Jeannel, 1937; Patrobonebria Bänninger, 1923, Paranebria Jeannel, 1937 and Barbonebriola Huber and Schmidt, 2017 = Epinebriola Daniel and Daniel, 1904; and Asionebria Shilenkov, 1982 = Psilonebria Andrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species: Nebria delicata Huber and Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species: Nebria carbonaria Eschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type species Nebria sahlbergii Fischer von Waldheim, 1828), Nivalonebria Kavanaugh subgen. nov. (type species: Nebria paradisi Darlington, 1931), Neaptenonebria Kavanaugh subgen. nov. (type species: Nebria ovipennis LeConte, 1878) and Palaptenonebria Kavanaugh subgen. nov. (type species: Nebria mellyi Gebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particulary within subgenera Leistus and Evanoleistus of genus Leistus and the Nebria Complex of genus Nebria.

opencc-zeroAug 2021View details →

ITS and nrLSU DNA sequence data from four species of Coreomyces (Laboulbeniomycetes)

The genus Coreomyces (Laboulbeniaceae, Laboulbeniomycetes, Ascomycota) includes minute parasites on water boatmen (Corixidae, Hemiptera, Insecta). This taxonomic study is primarily based on freshly sampled corixids infected by Coreomyces from Sweden, although a few samples from Denmark and Turkey were also included. All records were verified using DNA sequence data from the internal transcribed spacer region and large subunit of the nuclear ribosomal DNA repeat region. We recognise four species, two of which are new to science: Coreomyces confusus H. Sundb. et al. sp. nov., C. dextrorsus H. Sundb. et al. sp. nov., C. macropus Thaxt., and C. corixae Thaxt. C. corixae is a new record for Denmark, Sweden, and Turkey, while C. macropus is a new record for Denmark and Sweden. All four species can inhabit two different yet distinct positions on the host. We observe that morphology is affected by the position on the host and that different species sharing the same position on the host tend to be difficult or impossible to separate on morphology only. We conclude that species circumscriptions in Coreomyces must be based on the integration of molecular and morphological data.

opencc-by-4.0Dec 2006View details →

Figures 6–9 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figures 6–9. Automontage photographs of features of the Aleiodes buzurae-group. (6) A. buzurae, metasoma. (7)– (9) A. barnardae sp. n., habitus, face and metasoma, respectively.

opencc-by-4.0Dec 2006View details →

Figure 5 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figure 5. Two fragments of the ITS2 region aligned by eye showing marked differences between species in the Aleiodes buzurae-group. Asterisks and bold font indicate substitutions in length-conserved regions and lines show regions of length variation. Xs indicate uncertainty about number and identity of bases.

opennotspecifiedJul 2021View details →

FIGURE 1 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)

FIGURE 1. Isotype sheet of Senecio racemulifer (= Jacobaea racemulifera) kept at MW.

opencc-by-4.0Dec 2016View details →

Fig. 2 in Two new Oriental species of Paramanota Tuomikoski (Diptera: Mycetophilidae), with DNA sequence data

Fig. 2. Paramanota trilobata, new species (holotype). A, Hypopygium, dorsal view; B, Hypopygium, ventral view; C, Outlines of aedeagus and associated structures, dorsal view; D, Antennal flagellomere 4, lateral view. Scale bar = 0.1 mm. cr = cercus, gs d = dorsal lobe of gonostylus, gs m = median lobe of gonostylus, gs v = ventral lobe of gonostylus, gx = gonocoxa, gx l = ventral gonocoxal lobe, hp = hypoproct, tg 9 = tergite 9, tg 10 = tergite 10.

opencc-by-4.0Aug 2003View details →

Fig. 21 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling

Fig. 21. Strict consensus of 34 equally mostparsimonious trees obtained by a heuristic analysis of the combined data (nonmolecular characters plus IRBP2) described in this report. Bremer support and bootstrap values are provided above and below each branch, respectively. Outgroup taxa are indicated with asterisks. Parsimonyequivalent resolutions of the basal ingroup polytomy are illustrated in figure 19D, E, and F. Parsimonyequivalent resolutions of the ''other Marmosa'' + Micoureus polytomy are shown in figure 22.

opencc-zeroSep 2021View details →

Supplementary material 1 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691

Scripts used for metabarcoding analysis

opencc-zeroSep 2021View details →

Supplementary material 2 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691

Figure S1, Tables S1, S2

Figure 7 from: Maddison D, Ober K (2011) Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae). ZooKeys 147: 229-260. https://doi.org/10.3897/zookeys.147.1871

Figure 7 - Summary of relationships in Trechitae and related taxa. Branches (including those subtended by triangles) indicate monophyletic groups supported by the combined analyses and at least two of the genes; quadrangles indicate groups whose status is unresolved.

Figure 6 from: Maddison D, Ober K (2011) Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae). ZooKeys 147: 229-260. https://doi.org/10.3897/zookeys.147.1871

Figure 6 - Summary of subtribal and tribal relationships supported by individual genes. Triangles indicate monophyletic groups; quadrangles represent paraphyletic groups A 28S rDNA B 18S rDNA C wingless.

Figure 3 from: Maddison D, Ober K (2011) Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae). ZooKeys 147: 229-260. https://doi.org/10.3897/zookeys.147.1871

Figure 3 - Majority-rule consensus tree of trees sampled in Bayesian analysis, with branch lengths proportional to average branch lengths across trees that contain that branch, for 18S rDNA data. See caption of Fig. 2 for additional details.

Figure 5 from: Maddison D, Ober K (2011) Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae). ZooKeys 147: 229-260. https://doi.org/10.3897/zookeys.147.1871

Figure 5 - Majority-rule consensus tree of trees sampled in Bayesian analysis for all three genes analyzed together. Ovals on branches indicate support for the clade based upon Bayesian (left), maximum likelihood (center), and parsimony (right) analyses. Darkest tones indicate strongest support for (grays and black) or against (pinks) the clade, with values indicating posterior probability expressed as a percentage (Bayesian), or bootstrap percentage (likelihood and parsimony).

Figure 4 from: Maddison D, Ober K (2011) Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae). ZooKeys 147: 229-260. https://doi.org/10.3897/zookeys.147.1871

Figure 4 - Majority-rule consensus tree of trees sampled in Bayesian analysis, with branch lengths proportional to average branch lengths across trees that contain that branch, for the complete wingless data. See caption of Fig. 2 for additional details.