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opennotspecifiedDec 2023View details →

FIGURE 2 in Xenoacremonium palmarum sp. nov., a novel species associated with Phoenix dactylifera in Iran

FIGURE 2. Xenoacremonium palmarum (IRAN 1348C). a–b. 14-days colony on PDA (reverse and top). c–d. 14-days colony on CMA. e–f. 14-days colony on OA. g–i. Conidiophores and conidia mounted in lactophenol or lactophenol cotton blue. J–k. Conidia. Scale bars: g, j and k = 5 μm, h–i = 10 μm.

opennotspecifiedDec 2023View details →

FIGURE 1. Phylogenetic tree generated from a in Xenoacremonium palmarum sp. nov., a novel species associated with Phoenix dactylifera in Iran

FIGURE 1. Phylogenetic tree generated from a maximum likelihood (ML) analysis based on the combined tub2, tef1α and ITS sequences of Xenoacremonium strains. The tree was rooted using Stachybotrys chartarum CBS 129.13 as the out-group taxon. Bootstrap values obtained in maximum likelihood (ML) analysis equal or greater than 50% and Bayesian posterior probability values (BYPP) equal or greater than 0.5 are shown at the nodes, respectively.

opennotspecifiedFeb 2024View details →

Figure 3 in A novel host association of Idris Förster (Hymenoptera: Scelionidae) with description of a new species from India

Figure 3. Maximum likelihood tree for the species of Idris based on 493 bp of mt COI DNA gene sequence.

opennotspecifiedFeb 2024View details →

Figure 2 in A novel host association of Idris Förster (Hymenoptera: Scelionidae) with description of a new species from India

Figure 2. Idris hirsutus Sunita and Rajmohana sp. n. Female. (A) Lateral habitus. (B) Antenna. (C) Dorsal view of head. (D) Lateral view of mesosoma. (E) Dorsal view of head and mesosoma. (F) Dorsal view of metasoma. (G) Ventral view of metasoma. (H) Fore wing.

opencc-by-4.0Nov 2024View details →

Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic alterations, TMB, and PD-L1

Wallen ZD, Ko H, Nesline MK, Tierno M, Roos A, Schnettler E, Husain H, Sathyan P, Caveney B, Eisenberg M, Severson EA, Ramkissoon SH. Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic. Front Oncol. 2024 Nov 5;14:1473327. doi: <a href="https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2024.1473327">10.3389/fonc.2024.1473327</a>. ABSTRACT Introduction: Matching patients to an effective targeted therapy or immunotherapy is a challenge for  advanced and metastatic non-small cell lung cancer (NSCLC), especially when relying on assays that test one  marker at a time. Unlike traditional single marker tests, comprehensive genomic profiling (CGP) can  simultaneously assess NSCLC tumors for hundreds of genomic biomarkers and markers for immunotherapy  response, leading to quicker and more precise matches to therapeutics. Methods: In this study, we performed  CGP on 7,606 patients with advanced or metastatic NSCLC using the Illumina TruSight Oncology 500 (TSO  500) CGP assay to show its coverage and utility in detecting known and novel features of NSCLC. Results:  Testing revealed distinct genomic profiles of lung adenocarcinoma and squamous cell carcinomas and  detected variants with a current targeted therapy or clinical trial in >72% of patient tumors. Known associations  between genomic alterations and immunotherapy markers were observed including significantly lower TMB  levels in tumors with therapy-associated alterations and significantly higher PD-L1 levels in tumors with ALK,  MET, BRAF, or ROS1 driver mutations. Co-occurrence analysis followed by network analysis with gene  module detection revealed known and novel co-occurrences between genomic alterations. Further, certain  modules of genes with co-occurring genomic alterations had dose-dependent relationships with histology and  increasing or decreasing levels of PD-L1 and TMB, suggesting a complex relationship between PD-L1, TMB,  and genomic alterations in these gene modules. Discussion: This study is the largest clinical study to date  utilizing the TSO 500. It provides an opportunity to further characterize the landscape of NSCLC using this  newer technology and show its clinical utility in detecting known and novel facets of NSCLC to inform treatment  decision-making. DATA AVAILABILITY The data and code presented in the study are deposited in this Zenodo repository, accession number  13137232 (<a href="https://zenodo.org/record/13137232">https://zenodo.org/record/13137232</a>). Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Further data inquiries can be directed to the corresponding  author.

opencc-by-4.0Oct 2024View details →

Data from: Novel associations among insect herbivores and trees: drivers of occurrence and damage on pines and eucalypts

List of novel associations beteween insects and pine and eucalypt trees recorded in these study (each row represents a single novel association). We detail characteristics of the insect species involved in each novel association, indicating their order, family, subfamily species, native biogeographic region (Afr: Afrotropic, AP: Austro-Pacific, IM: Indo-Malaya, Nea: Nearctic, Neo: Neotropic, Pal: Palearctic), non-native biogeographic region where it has established, feeding guild (W&PF: wood and phloem feeder, FF: foliage feeder, F&SF: fruit and seed feeders , SF: sap feeder, ShF: shoot feeder), specificity in host use (VP: very polyphagous, P: polyphagous, O: oligophagous, M: monophagous), impact (N: negligible, L-M: low-medium, H: high, LD: lack of data), and the tree condition (L: living, DD: dying or dead, D: exclusively dead). Information not available is indicated as N/A). We also detail the biogeographic region where the novel association was reported, the novel association type (NIET: native insect on exotic trees, EINT: exotic insect on native trees, EIET: exotic insect on exotic trees), the pine and eucalypt novel host involved in the association, and the phylogenetic relatedness between ancient and novel hostts both for pines and eucalypts (SG: same genus, SF: different genera of the same family, DF: different family). Colors were assigned for the  insect species involved in: two new association (orange), three new association (yellow), four new association (pink), five new association (green).

opencc-by-4.0Oct 2023View details →

Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture

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opencc-by-4.0May 2024View details →

Genome annotations for: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes

<div> Peter Thorpe1, Simone Altmann1, Rosa Lopez-Cobollo2, Nadine Douglas3, Javaid Iqbal2, Sadia Kanvil2, Jean-Christophe Simon4, James C. Carolan3, Jorunn Bos1*, Colin Turnbull2*  </div> <div> 1School of Life Sciences, University of Dundee, UK; 2Department of Life Sciences, Imperial College London, UK; 3Department of Biology, Maynooth University, Republic of Ireland; 4 INRAE , France. *Authors for correspondence: <a href="mailto:j.bos@dundee.ac.uk" target="_blank" rel="noreferrer noopener">j.bos@dundee.ac.uk</a>, <a href="mailto:c.turnbull@imperial.ac.uk" target="_blank" rel="noreferrer noopener">c.turnbull@imperial.ac.uk</a>.     This is a repository for the version3 gene predictions and annotation for the pea aphid used for the publication:   Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes    <div> ABSTRACT </div> <div> Background. Compatibility between aphids and plant hosts is genetically determined by both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes.  </div> <div> Results. We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 resistance quantitative trait locus. Differential expression analysis based on RNA sequencing of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence/avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some of the differentially expressed transcripts were also found in the differentially expressed proteomes, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (26%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.   </div> <div> Conclusions. Especially when combined with tightly controlled genetics of both insect and host, multi-omic approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.  </div> </div>

opencc-by-4.0Jul 2024View details →

Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-Function ATP13A2 Variant and Response to Antipsychotic Therapy

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Supplementary material 3 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Table S1 : Explanation note: List of measurements of teliospore characters of R.evansii. Obtained values were sorted by voucher and by individual teliospores. All measurements are given in μm.

Supplementary material 4 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Table S2 : Explanation note: List of measurements of teliospore characters of R.macowaniana and R.xanthophloeae. Obtained values were sorted by voucher and by individual teliospores. All measurements are given in μm.

Supplementary material 2 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Figure S2 : Explanation note: Boxplot of measurements of the six defined teliospore characteristics of R.macowaniana and R.xanthophloeae. Values were obtained from teliospores derived from three different host species of in total 10 individual trees. The boxplots are based on mean values calculated for all investigated teliospores for each specimen, respectively.

Supplementary material 1 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Figure S1 : Explanation note: Boxplot of measurements of the six defined teliospore characters of R.evansii. Values were obtained from teliospores derived from seven different host species of in total 18 individual trees. The boxplots are based on mean values calculated for all investigated teliospores for each specimen, respectively.

opennotspecifiedMay 2024View details →

FIGURE 2 in Hermatomyces pyriformis sp. nov., a novel dematiaceous hyphomycete (Hermatomycetaceae, Pleosporales) associated with medicinal plants in Yunnan Province, China

FIGURE 2. Hermatomyces pyriformis (HKAS 132457, holotype). a. Host Eleutherococcus nodiflorus. b. Branch of Eleutherococcus nodiflorus. c−e. Colonies on host surface. f. Conidiophores with conidia. g, h. Colonies on PDA (g from above, h from below). i−l. Conidiogenous cells and conidia. m. Germinated conidium. n−u. Conidia. Scale bars: f, i−u = 10 µm.

opennotspecifiedMay 2024View details →

FIGURE 1 in Hermatomyces pyriformis sp. nov., a novel dematiaceous hyphomycete (Hermatomycetaceae, Pleosporales) associated with medicinal plants in Yunnan Province, China

FIGURE 1. Phylogenetic tree from ML analysis based on the combined LSU, ITS, tef1-α and rpb2 sequences data. Branches support for ML ≥ 75% and Bayesian inference posterior probabilities (BIPP) ≥ 0.95 are marked above or below branches as MLBS/BIPP. The tree was rooted with Elsinoe centrolobi (AFTOL-ID 1854) and E. veneta (AFTOL-ID 1360). The abbreviation T indicate ex-type isolates. New species is indicated in red.

opencc-by-4.0Sep 2024View details →

AntiSMASH results of the genome sequences of four novel Endozoicomonas strains associated with the octocoral Litophyton in a long-term aquarium facility

Secondary Metabolite-Encoding Biosynthetic Gene Cluster (SM-BGC) annotation files from antiSMASH bacterial version 7.1.0 for four Endozoicomonas strains associated with the tropical octocoral Litophyton in a long-term aquarium facility. Data corresponds to the assemblies of NE35, NE40, NE41 and NE43, available under the BioProject accession numbers <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075803">PRJNA1075803</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075804">PRJNA1075804</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075805">PRJNA1075805</a> and <a href="https://www.ncbi.nlm.nih.gov/bioproject/1075806">PRJNA1075806</a>, respectively. To easily and interactively review the results, please download the genome you wish to examine, extract the entire contents of the folder, and open the HTML file named "Results".   This dataset is part of the following study: Marques M, da Silva DMG, Santos E, Baylina N, Peixoto R, Kyrpides NC, Woyke T, Whitman WB, Keller-Costa T, Costa R. 2024. Genome sequences of four novel Endozoicomonas strains associated with a tropical octocoral in a long-term aquarium facility. Microbiology Resource Announcements

FIGURE 5 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China

FIGURE 5. Wongia bambusae (HKAS 127154 holotype) a–l Colonies on natural substrate. a–b Colonies. c–e Conidiophores and conidia. f–g Conidiogenous cells. h–l Conidia. m Germinating conidium. n, o Colony on PDA from above and below. p–u Sporulation observed on PDA. p, q Conidiophores and conidia. r–u Conidia. Scale bars: c–e = 20 μm, f–h, p, q = 10 μm, i–m, r–u = 5 μm.

FIGURE 4 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China

FIGURE 4. Conlarium guizhouense (HKAS 127152) a–m Colonies on natural substrate. a–c Colonies. d, i–m Conidia. e–h Conidiogenous cells and conidia. n, o Colony on PDA from above and below. p–u Sporulation observed on PDA. p, q Conidiogenous cells and conidia. r–u Conidia. Scale bars: d = 20 μm, e–m, p–u = 10 μm.

FIGURE 3 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China

FIGURE 3. Conioscypha sichuanensis (HKAS 127153 holotype). a–j Colonies on natural substrate. a–c Colonies. d–g Conidia and conidiogenous cells with cup-shaped multi-collarette. h–i Conidia and conidiogenous cell. j Conidia. k Germinating conidium. l, m Colony on PDA from above and below. n–t Sporulation observed on PDA. n–p Conidia and conidiogenous cell. q–t Conidia. Scale bars: k = 20 μm, d–j, n–p = 10 μm, q–t = 5 μm.

FIGURE 1 in Novel hyphomycetous fungi associated with bamboo from Sichuan, China

FIGURE 1. RAxML tree generated from combined SSU, ITS, LSU, rpb2 and tef1α sequence data of targeted six families (Acrodictyaceae, Atractosporaceae, Conlariaceae, Papulosaceae, Pseudoproboscisporaceae and Pseudostanjehughesiaceae) in Diaporthomycetidae. The tree is rooted with Cancellidium cinereum (MFLUCC 18-0424) and C. griseonigrum (MFLUCC 17-2117). Ex-type strains are indicated in bold and newly generated sequences are in red. Bootstrap values for ML equal to or greater than 75% are placed above the branches. Branches with Bayesian posterior probabilities (BYPP) from MCMC analysis equal to or greater than 0.95 are in bold.