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opennotspecifiedNov 2022View details →

Fig. 1 in Genetic variation in the spotted seal (Phoca largha Pallas, 1811) from the Rimsky-Korsakov Archipelago (Peter the Great Bay, western sea of Japan) as inferred from mitochondrial DNA control region sequences

Fig. 1. Map of the Phoca largha sampling site.

opencc-zeroApr 2024View details →

Chisholm Lake sedimentary unprocessed fish metabarcoding DNA sequences

We sequenced amplicons targeting a segment of the 12S ribosomal DNA gene in vertebrates from DNA pools isolated from sections of a sediment core from Chisholm Lake in interior Alaska. The primary aim of this sequencing effort was to add to our understanding of the evolution of fish faunas in Beringian regions impacted by glacial cycles. This dataset consists of unprocessed output from amplicon paired end short read sequencing on an Illumina sequencing by synthesis platform. Analyses of these sequences are being incorporated into a broader effort to examine post-glacial Beringian biotas and ecologies.

opencc-by-4.0Jan 2021View details →

Figures 19–23 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi

Figures 19–23: Chamberlainium glebosum habit and vegetative anatomy. (19) Rock fragment with holotype specimen showing the region (white arrow) of the holotype from which all analyses were done (L 3986123, tetrasporangial). Scale bar = 20 mm. (20) Magnified view showing highly protuberant nature of C. glebosum holotype specimen (L 3986123). Scale bar = 2 mm. (21) Vertical section through the margin (black arrow) showing the monomerous thallus construction with plumose medulla (M) giving rise to cortical filaments (C) that terminate in a single layer of epithallial cells (black arrowhead) (UWC 15/34). Scale bar = 100 μm. (22) Vertical section of the inner thallus showing cell fusions (f) between adjacent medullary filaments (UWC 15/34). Scale bar = 10 μm. (23) Vertical section of the outer thallus showing a single layer of epithallial cells (e) subtended by a layer of subepithallial initials (i). Note the cell fusions (f) between adjacent cortical filaments (UWC 15/34). Scale bar = 20 μm.

opencc-by-4.0Apr 2024View details →

Nanomotif: Identification and Exploitation of DNA Methylation Motifs in Metagenomes using Oxford Nanopore Sequencing

Open the record for dataset details and reuse information.

opencc-by-4.0Feb 2021View details →

Mullus surmuletus environmental DNA intraspecific metabarcoding Next-Generation Sequencing data

Four 250-liter aquariums were bleached clean one day prior to be used (filled with seawater; fish transfer) in Montpellier (France). Seawater collected by the French Research Institute for Exploitation of the Sea at Palavas-les-Flots (France) was first stored in a 1,000 L tank for two weeks, under UV treatment to avoid any contamination. The aquariums were then filled with 120 L of this water. Each aquarium had a closed-circuit water circulation and was equipped with an air bubbles exhauster in a tube that brought up the water on a neutral synthetic foam filter. The aquariums were thus oxygenated and the coarsest suspended matter was filtered out. The remaining seawater in the tank was used as a negative control (Aquarium 1). Nine to eleven fish were added to each of the four aquariums (Fig. 1). The aquarium water was sampled six hours after introducing the fish into the aquariums using an Athena peristaltic pump (SPYGEN, Le Bourget-du-Lac, France) with a nominal flow of 1.0 L/min to filter 30 L, and VigiDNA 0.22 μm crossflow filtration capsules (SPYGEN) with disposable sterile tubing. After filtration, 80 mL of CL1 conservation buffer (SPYGEN) was added before storing the samples at ambient temperature.   We reanalyzed here two eDNA samples of 30 L replicate each, collected in  the Mediterranean Sea, at Banyuls (France, coordinates: 42.41568, 3.17110) and Calvi (France, coordinates: 42.62964, 8.89161) published in a previous metabarcoding analysis and known to contain M. surmuletus sequences (detected with the metabarcode teleo 12S) (Boulanger et al. 2021). These two Mediterranean eDNA samples were amplified and sequenced using the primers developed for this study and then analyzed using the best-performing pipeline as determined by our evaluation. These two samples were used as proof of concept of the possibility to estimate within site variability in real conditions.     DNA extraction and amplification from eDNA samples were performed by the company SPYGEN (Le Bourget du Lac, France) in separate, dedicated rooms following the protocol described by Polanco Fernández et al. (2020). The amplification was performed in a final volume of 25 μL including 1 U of AmpliTaq Gold DNA Polymerase (Applied Biosystems, Foster City, CA, USA), 10 mM of Tris-HCl, 50 mM of KCl, 2.5 mM of MgCl2, 0.2 mM of each dNTP, 0.2 μM of each primer, 0.2 μg/μL of bovine serum albumin (Roche Diagnostics, Basel, Switzerland) and 3 μL of DNA template. The PCR mixture was denatured at 95°C for 10 min, followed by 50 cycles of 30 s at 95°C, 30 s at 47°C and 1 min at 72°C and a final elongation step at 72°C for 7 min.  The primers were 5’-labelled with an eight-nucleotide tag unique to each DNA sample, allowing each sequence to be assigned to the corresponding sample during the sequence analysis. Twelve replicate PCRs were run per sample. Two libraries were prepared using the MetaFast protocol (Fasteris 2020, <a href="https://www.fasteris.com/dna/">https://www.fasteris.com/dna/</a>) and the sequencing was performed by Fasteris (Geneva, Switzerland) on two separate runs on an Illumina MiSeq (2x250 bp) (Illumina, San Diego, CA, USA) and the Miseq Kit v3 (Illumina) following the manufacturer’s instructions. Two negative extraction controls and one negative PCR control (12 replicates of ultrapure water) were amplified and sequenced to monitor for possible contaminants (Polanco Fernández et al., 2020).

opencc-zeroNov 2021View details →

Oxylobus (Asteraceae) analysis DNA sequence data

A molecular phylogenetic investigation was carried out to clarify aspects of the systematics of Oxylobus, a primarily Mexican alpine genus of Eupatorieae. Analysis of sequence data from two nuclear (nrDNA ITS, ETS) and three plastid markers (rbcL, ndhF, matK) confirmed the monophyly of Oxylobus and placed species of Ageratina as its sister group. A survey of 56 samples of Oxylobus using nrDNA ITS and ETS provided support for the currently accepted species, and showed the recently described O. coyulensis to be distinct and the sister group to the rest of the genus. The results also confirmed the placement of O. juarezensis in synonymy with O. subglabrus. The results of a broad survey of Ageratina for ITS data showed that it is likely not monophyletic as currently circumscribed. The phylogenetic results also highlighted the distinctiveness of Piqueria and Piqueriopsis as a distinct clade at the base of Eupatorieae.

opencc-zeroDec 2021View details →

OTUs Table and fastq sequences from environmental DNA applied to trematode communities

This OTUs table and fastq sequences underlie the main results of the study "Make visible the invisible: Optimized development of an environmental DNA metabarcoding tool for the characterization of trematode parasitic communities". In this study, our aim was to develop an optimized eDNA-based metabarcoding approach to detect trematodes and characterize their communities, most of which associated to aquatic environments. We thus assessed the ability of our eDNA-based metabarcoding approach to reconstruct trematode communities compared to a classical trematode monitoring method over four freshwater aquatic ecosystems. We focused on 4 natural sites from Occitanie Region (Southern France) that differ in terms of habitats, and in which the trematode communities were previously at least partially characterized. At each of these sites, we sampled the water-sediment interface from which the eDNA was extracted and sequenced with a MiSeq amplicons sequencing approach. Over the four natural ecosystems screened in nature, 33 OTUs were generated from the eDNA-based approach, from which 11 trematode species were identified. In comparison, we identified five trematode species using the classical monitoring method, three of which were also detected by the eDNA-based approach.

opencc-zeroFeb 2022View details →

DNA sequence data use in phylogenetic analysis of eastern North American stitchworts

Generic delimitation in Caryophyllaceae has been a challenge, and has been informed most recently by use of molecular phylogenetic data. In this study, analysis of 29 samples from the small segregate Mononeuria using nuclear ITS and plastid rps16 data revealed it to be polyphyletic. The type species Mononeuria patula as well as two others (M. muscorum and M. paludicola) were shown to belong to the Sabulina clade. The remaining species formed a clade that also included the previously monotypic Geocarpon and was sister to a heterogeneous group that included the Hawaiian Schiedea and three other monotypic genera, Honckenya, Wilhelmsia, and Triplateia. Although several nomenclatural options are available, we propose to place the species from this clade into a single genus, Geocarpon, which basically follows the most recent treatment after exclusion of Sabulina species, but with the necessary new genus placements. New combinations are proposed: Sabulina muscorum, Sabulina paludicola, Geocarpon carolinianum, Geocarpon cumberlandensis, Geocarpon glabrum, Geocarpon groendlandicum, Geocarpon nuttallii, and Geocarpon uniflorum. Analysis of the sequence data revealed remarkable variability among populations of Sabulina (formerly Mononeuria) patula, Sabulina (formerly Mononeuria) paludicola, and Geocarpon (formerly Mononeuria) groenlandicum, suggesting that cryptic species may be present. The data also suggested that broader sampling of Sabulina and Geocarpon could lead to increased understanding of the timing and origins of occupation of calcareous glades and rock outcrop habitats in eastern North America.

opencc-zeroFeb 2022View details →

DNA sequence data - Bicyclus

Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the continent. By investigating the evolutionary history of Bicyclus butterflies within a phylogenetic framework, we inferred the group's origin at the Oligo-Miocene boundary from ancestors in the Congolian rainforests of central Africa. Abrupt climatic fluctuations during the Miocene (ca. 19–17 Ma) likely fragmented ancestral populations, resulting in at least eight early-divergent lineages. Only one of these lineages appears to have diversified during the drastic climate and biome changes of the early Miocene, radiating into the largest group of extant species. The other seven lineages diversified in forest ecosystems during the late Miocene and Pleistocene when climatic conditions were more favorable—warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa.

opencc-by-4.0Mar 2022View details →

Data related to the manuscript "Sequence-specific aggregation of magnetic nanoparticles and single-stranded DNA amplification products for detection of antibiotic resistance gene sul1."

Absorbance and AC susceptometry raw and processed excel files used.

opencc-by-4.0Sep 2019View details →

Fig. 2 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species

Fig. 2. Phylogenetic position of E. roumanicus, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.

opencc-zeroJun 2022View details →

Supplementary material 2 from: Naro-Maciel E, Ingala MR, Werner IE, Reid BN, Fitzgerald AM (2022) COI amplicon sequence data of environmental DNA collected from the Bronx River Estuary, New York City. Metabarcoding and Metagenomics 6: e80139. https://doi.org/10.3897/mbmg.6.80139

Tables S1,S2, Figures S1–S3

opencc-zeroJun 2022View details →

Supplementary material 1 from: Naro-Maciel E, Ingala MR, Werner IE, Reid BN, Fitzgerald AM (2022) COI amplicon sequence data of environmental DNA collected from the Bronx River Estuary, New York City. Metabarcoding and Metagenomics 6: e80139. https://doi.org/10.3897/mbmg.6.80139

Supplementary Data Files 1, 2

opencc-zeroDec 2016View details →

Data from: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Lactose provides an easily-digested energy source for neonate mammals, and is the primary carbohydrate in milk. Lactose is also a key component of many human food products, though compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS of milk lactose concentration and yield, investigated in a population of 12,000 taurine dairy cattle. We detail 27 QTL spanning these traits, and subsequently validate the effects of 26 of these loci in a separate population of 18,000 cows. We next present data implicating causative genes and variants for these QTL. Fine mapping of these regions using imputed, whole genome sequence-resolution genotypes reveals protein-coding candidate causative variants affecting the ABCG2, DGAT1, STAT5B, KCNH4, NPFFR2 and RNF214 genes. Eleven of the remaining QTL appear to be driven by regulatory effects, suggested by the presence of co-locating, co-segregating eQTL discovered using mammary RNA sequence data representing a population of 357 lactating cows. Pathway analysis of genes representing all lactose-associated loci shows significant enrichment of genes located to the endoplasmic reticulum, with functions related to ion channel activity mediated through the LRRC8C, P2RX4, KCNJ2 and ANKH genes. Together, these findings highlight novel candidate genes and variants involved in milk lactose regulation, whose impacts on facilitated and active membrane transport mechanisms reinforce the key osmo-regulatory roles of lactose in milk.

opencc-zeroDec 2013View details →

Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the ITS region, frequently used in plant phylogenetics, is now recognised as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analysed datasets from the Saccharomyces Genome Resequencing Project, characterising rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterisation of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intra-species phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridisation events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multi-locus rDNA systems.

Figure 7 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655

Figure 7 - Kibaleana apicospinosa sp. n., male terminalia. A Dorsal view B Tergite IX and cerci, dorsal view C Tergite IX, cerci and hypoproct, ventral view D Male terminalia, dorsal view, tergite IX detached E Aedeagal complex, dorsal view F Medial part of gonocoxite, ventral view G Basal part of gonostylus, dorsal view H Apical part of gonostylus, ventral view. Abbreviations: aed = aedeagus; aed ap = aedeagal apodeme; cer = cercus; ej ap = ejaculatory apodeme; gc = gonocoxite; gc ap = gonocoxal apodeme; gc vmp = ventromedial process of gonocoxite; gst = gonostylus; gst bp = basal process of gonostylus; hyp = hypoproct; par = paramere; par ap = parameral apodeme; tg 9 = tergite IX.

Figure 4 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655

Figure 4 - Kibaleana apicospinosa sp. n., male. A Head, frontal view B Compound eye, closer view C Head, frontal view D Maxillary palpus, posterior view. Abbreviations: clyp = clypeus; eye = compound eye; fc = face; flgm = flagellomeres; fr = frons; lbl = labellum; lin = lingua; l oc = lateral ocellus; m oc = medial ocellus; ped = pedicel; plp = segments of maxillary palpus; scp = scape.

Figure 6 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655

Figure 6 - Kibaleana apicospinosa sp. n., apical part of tibia and basal part of first tarsal segment, male. A Fore leg B Mid leg C Hind leg D Fore leg, closer view. Abbreviations: acmb = apical comb of setae; t = fore, mid and hind tibiae.

Figure 3 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655

Figure 3 - Kibaleana apicospinosa sp. n., male. A General habitus, lateral view B Head and thorax, lateral view C Fourth segment of flagellum, lateral view D Head, lateral view E Claw, lateral view F Claw, dorsal view. Abbreviations: abd = abdomen; anepst = anepisternum; anepm = anepimeron; aprnt = antepronotum; cx = coxa; eye = compound eye; flgm = flagellar segment; fr = frons; hlt = halter; ltg = laterotergite; mtepst = metepisternum; mtg = mediotergite; mx plp = maxillary palpus; oc tr = ocellar triangle; ped = pedicel; png = postgena; preepst 2 = preepisternum 2; sc = scutum; scp = scape; vrt = vertex; wg = wing.

Figure 5 from: Kurina O, Mantič M, Ševčík J (2017) A remarkable new genus of Keroplatidae (Insecta, Diptera) from the Afrotropical region, with DNA sequence data. African Invertebrates 58(1): 93-105. https://doi.org/10.3897/afrinvertebr.58.12655

Figure 5 - Kibaleana apicospinosa sp. n., male. A Wing, dorsal view B Head and thorax, dorsal view. Abbreviations: A = anal vein; acr s = acrostichal setae; C = costal vein; Cu = branches of cubitus; dc s = dorsocentral setae; h = humeral vein; l s = lateral setae; M = branches of media; m-cu = medio-cibital crossvein; mtg = mediotergite; R = branches of radius; r-m = radio-medial crossvein; Sc = subcostal vein; sc = scutum; sctl = scutellum; tb = basal transversal.