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2,145 results for “Linnaeus”
Draft genome assembly version 1 of the meadow spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae)
<p>We sequenced the genome of the meadow spittlebug, <em>Philaenus spumarius </em>(Linnaeus, 1758), the main insect vector of <em>Xylella fastidiosa </em>Wells et al. 1987 in Europe (Saponari et al., 2014), using 10x Chromium linked-reads. A single <em>P. spumarius</em> adult female from Portugal (Fontanelas, Sintra; GPS location: 38°50'15.75"N; 9°25'20.77"W), collected in September of 2018, was selected for genome sequencing. This population was initially surveyed for colour polymorphism in 1988 (Quartau & Borges, 1997) and was later included in phylogeographic and population genomic studies of this species (Rodrigues et al., 2014; Seabra et al., unpublished). It is also geographically close to the population from which the individual used for the first partial genome assembly was collected (Rodrigues et al., 2016). The availability of this previous genetic information contributed to the choice of this population as the source of genomic material for whole genome sequencing. A subset of males from the same collection date were analysed for genitalia morphology to confirm species identification, as the best diagnostic characters are the appendages of the aedeagus (Drosopoulos & Quartau, 2002).</p> <p>The genomic DNA of the <em>P. spumarius</em> adult from Sintra was extracted using Illustra Nucleon Phytopure kit according to the manufacturer’s instructions (GE Healthcare). We assessed the quality and concentration of the DNA using Femto fragment analyser (Agilent). 10x Chromium library preparation and Illumina genome sequencing (HiSeq X, 150bp paired-end) were performed by Novogene Bioinformatics Technology Co, Beijing, China, in accordance with standard protocols.</p> <p>To create the <em>de novo</em> 10x Chromium assembly we ran Supernova 2.1.1 (Weisenfeld et al., 2017) on the 10x Chromium linked-read data with default parameters, using 1.0 billion reads corresponding to 56X coverage. To improve the initial supernova assembly, we performed iterative scaffolding using all of the 10x raw data (2.3 billion of reads). We ran two rounds of Scaff10x (https://github.com/wtsi-hpag/Scaff10X), followed by mis-assembly detection and correction with Tigmint (Jackman et al., 2018). This was followed by a final round of scaffolding with ARCS (Yeo et al., 2018). The assembly was checked for contamination using the BlobTools pipeline (version 0.9.19; Laetsch and Blaxter 2017; Kumar et al., 2013) and k-mer content was analysed with the KAT comp tool (Mapleson et al., 2017). In order to perform these analyses, it was necessary to remove the 10x linked barcodes from the reads with the script process_10xReads.py (https://github.com/ucdavis-bioinformatics/proc10xG). We assessed the quality of our draft genome assembly by searching for conserved, single copy, arthropod genes (n=1,066) with Benchmarking Universal Single-Copy Orthologs (BUSCO) v3.0 (Waterhouse et al., 2018).</p> <p>With the above assembly procedure, we obtained a final assembly of 2.7 Gb, having a scaffold N50 length of 116 Kb (contig N50 = 18 Kb) and the longest scaffold was 3.7 Mb. The length of the assembly was consistent with the genome size estimated by flow cytometry (Rodrigues et al., 2016). The k-mer distribution indicated high heterozygosity, estimated at 2.3%. BlobTools analyses revealed the presence of contigs assigned to <em>Sodalis </em>spp. (Enterobacteriaceae), a symbiont in members of tribe Philaenini (Koga et al., 2013). These contigs were filtered from the final assembly. Gene completeness assessment shows that 956 (89.6%) among 1,066 BUSCOs were found as complete copies, with only 26 (2.4%) missing. Of the BUSCOs that were detected, 878 (82.4%) were complete and single-copy, 78 (7.3%) were complete and duplicated and 84 (7.9%) were fragmented.</p> <p>In conclusion, due in part to high (2.3%) heterozygosity levels, the <em>P. spumarius</em> version 1 genome assembly is highly fragmented. Nonetheless, the assembly is considered complete and is likely to contain the majority of the gene content of <em>P. spumarius.</em></p>
Herbarium specimen image of Odonthalia dentata (Linnaeus) Lyngbye, part of the collection of Royal Botanic Garden Edinburgh
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Fig. 3 in Relationships between fish and otolith dimensions of Pomatomus saltatrix (Linnaeus, 1766) (Perciformes: Pomatomidae) in southeastern Brazil
Fig. 3. Absolute and cumulative frequency of individuals by length class (cm) (a) and total weight of individuals by length class and condition factor (k) (b) of Pomatomus saltatrix, obtained from commercial catches off the Brazilian coast in the Southeastern Atlantic Ocean.
Fig. 1 in Relationships between fish and otolith dimensions of Pomatomus saltatrix (Linnaeus, 1766) (Perciformes: Pomatomidae) in southeastern Brazil
Fig. 1. Map of sampling area, hatched area identifies where catches of Pomatomus saltatrix occurred, off the Brazilian coast in the Southeastern Atlantic Ocean.
FIG. 4 in A zooarchaeological study of Rangifer tarandus (Linnaeus, 1758) from the Croxton site in Brooks Range, Alaska, and implications for utility analysis
FIG. 4. — Split caribou (Rangifer tarandus (Linnaeus, 1758)) right metatarsal with impacts on opposing surfaces. After being split and discarded, the bone
FIG. 1 in A zooarchaeological study of Rangifer tarandus (Linnaeus, 1758) from the Croxton site in Brooks Range, Alaska, and implications for utility analysis
FIG. 1. — Map showing the locations of the Croxton archaeological site and the modern village of Anaktuvuk Pass along the north slope of the Brooks Mountain Range, Alaska, United States.
FIG. 11. — A in The modern ontological natures of the Cairina moschata (Linnaeus, 1758) duck. Cases from Perú, the northern hemisphere, and digital communities
FIG. 11. — A, logo of D'Artagnan Foods Inc. Image via Wikimedia Commons; B, poster of campaign to stop the expansion of foie gras industry in China (https:// safarus.wordpress.com/2012/03/24/chinese-activists-call-for-boycott-of-the-largest-foie-gras-farm, last consultation: 06/09/2019).
FIGURE 131. Ostracion cubicus Linnaeus 1758 in The marine ichthyofauna of Lebanon: an annotated checklist, history, biogeography, and conservation status
FIGURE 131. Ostracion cubicus Linnaeus 1758, Beirut, 2 November 2015, AUBM (OS3913), Crocetta & Bariche in Dailianis et al. (2016).
FIG. 3 in A model for llama (Lama glama Linnaeus, 1758) domestication in the southern Andes
FIG. 3. — Representation of regional archaofaunas (% NISP), and time-trends for Camelidae, and Chinchillidae. Camelids increase over time, meanwhile the other animal resources diminishes.
FIG. 3 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 3. — Évolution du nombre de loutres capturées en Belgique durant les mois de novembre entre 1889 et 1921.
FIG. 5 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 5. — Répartition des fréquences d'apparition des individus au sein des captures en fonction de leur degré de maturité sexuelle. Abréviations: A, adulte; J, juvénile; NA, information non disponible.
FIG. 7 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 7. — Variations inter-mensuelles des captures (une capture peut concerner plusieurs individus). NA, information non disponible.
FIG. 4 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 4. — Répartition des fréquences d'apparition des individus au sein des captures en fonction de leur sexe. F, femelles; M, mâles; NA, information non disponible.
FIG. 6 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 6. — Fréquence d'apparition des lieux de captures (une capture peut concerner plusieurs individus. NA, information non disponible).
FIG. 11. — Capture d in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 11. — Capture d'une loutre mâle de 6 kg prise au piège le 27 février 1942 par le garde Waldor Magerat à Lessines (province du Hainaut) (Anonyme 1942: 38).
FIG. 8 in La loutre (Lutra lutra Linnaeus, 1758) en Belgique: une espèce mal-aimée et malmenée (19 -début 20 siècles)
FIG. 8. — Fréquence d'apparition des techniques de captures (une capture peut concerner plusieurs individus).
Fig. 2 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species
Fig. 2. Phylogenetic tree of the Bayesian Inference of the Bagre derived from the concatenated database of the Cytb 1 and ATPase 8/6 genes. Only unique haplotype are included here. The first value on each branch corresponds to the ML support value and the second one to the BI. Only support values and posterior probabilities above 60% are shown. Grey = northern Brazilian coast lineage, including the semi-arid sector of the northeast coast; Black = southern Brazilian coast.
Fig. 6 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species
Fig. 6. Scatterplots of the principal components PC1 and PC2, obtained from the analysis of one meristic and nine morphometric variables in Bagre bagre, with factor loadings for the first principal components. Abbreviations: E, east Brazilian coast; h, humid northeastern coast of Brazil; N, northern Brazilian coast; sa, semi-arid northeastern coast of Brazil; S, southeast Brazilian coast.
Fig. 4 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species
Fig. 4. Genealogiesofthehaplotypesof (A) themitochondrial Cytb gene, based on the TIM2+I+G evolutionary model, and (B) the mitochondrial ATPase 8/6 gene, based on the HKY+G model. Green = northern Brazilian coast influenced by the Amazon–Orinoco plume, Light blue = semi-arid northeastern coast, Orange = southeastern coast.
Fig. 1 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species
Fig. 1. Geographic distribution of the two Bagre bagre lineages found in South America [red triangle = northern Brazilian coast, including region dominated by the plume of the Amazon and Orinoco rivers and semi-arid sector of Brazilian northeast coast (light blue = mouth of the Orinoco River; black circle = Macapá, AP; dark blue circle = Bragança, PA; yellow = São Luis, MA; green = Fortaleza, CE), and inverted black triangle = eastern and southern Brazilian coast, including the humid sector of the northeast coast (white circle = Santos, SP)] showing the number of specimens analyzed in each region (not bold = morphological analysis, and bold = molecular analysis). Green = northern Brazilian coast influenced by the Amazon– Orinoco plume, Light blue = semi-arid northeastern coast of Brazil; Dark blue = humid northeastern coast of Brazil, Yellow = east coast, and Orange = southeast coast).
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OpenNeuro
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