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Fig. 2 A in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 2 A Manhattan plot of the V. arizonica genome showing markers associated with bacterial load. The plot denotes each of the 19 chromosomes for haplotype 1. Each circle represents a SNP with a corresponding p value, based on EMMAX genome-wide association analysis. The 25 SNPs that were detected in two separate GWA analyses are circled in red and define the 8 peaks of association, which are numbered as P1, P2, etc., and referred to in the text. In addition to SNPs, the locations of significantly associated kmers and CNVs are provided when they overlap with a SNP-defined peak. The colored horizontal lines represent the cut-off p-values (P <0.05, Bonferroni corrected) for the different marker types. Significant (P <0.05, Bonferroni corrected) kmers and CNVs are represented by red and blue triangles, respectively.

Fig. 1 Vitis arizonica sampling and phenotypes. A in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 1 Vitis arizonica sampling and phenotypes. A map of the Southwestern United States and Northern Mexico indicates sampling locations of the n = 167 V. arizonica accessions used in this study. The color of sample locations (circles) are colored according to their resistance phenotype, as measured by bacterial load (CFU/mL). The histogram of phenotypes (in CFU/mL) is to the right of the map. Map generation relied on information from GADM, a publicly available database (http:gadm.org).

Fig. 5 in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 5 Relationships among resistance, genetic markers and bioclimatic data. a The estimated relative importance, from GF modeling, of each of the bioclimatic variables tested. The y-axis is a measure of the importance of various variables to explain the model - i.e., the relative importance of each bioclimatic variable for predicting changes in allele frequency across the landscape. Each boxplot denotes the average inferred importance of the bioclimatic variable, with the whiskers plotting the standard deviation of 1000 separate analyses (gray dots). BIO8 was estimated to have the biggest impact on the model in all 1000 analyses. b The turnover function showing the temperature range of BIO8 on the x-axis and the change in the genetic composition on the y-axis. The circles represent individuals that are colored by resistance (gray) or susceptible (white). c Individual predictors in a linear model to predict resistance levels (CFU/ml). The label score_ref represents sets of 1000 randomly chosen sets of 25 SNPs; K1 and K2 are the proportion of the assignments to each admixture group for each individual. The other predictors include bioclimatic variables and genomic data, as listed in the text, each evaluated 1000 times with bootstrapped datasets. Each boxplot reports the second and third quartiles, with median values in the square and circles showing outliers. The barplot whiskers report standard deviation, and the dashed horizontal line reflects the median value of 1000 replicates of the Rpd score. d The density distribution of BIO8 for a global database of locations of Xylella fastidiosa detection.

Fig. 4 in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 4 The presence of resistance and susceptibility kmers in different data sets. a Analyses within the V. arizonica sample set. The top-left graph indicates the 99 different resistance (R-kmers) kmers across the x-axis, with their detection frequency across the resistant (CFU/mL <13) accessions. The top-right graph plots the average detection frequency of susceptibility kmers (S-kmers). The bottom-left and bottom-right graph are similar, they but show R-kmer and S-kmer detection frequencies among susceptible accessions. b The same graphs as in A, but the top graphs plot R-kmer and S-kmer detection frequencies for the five V. vinifera cultivars bred for PD resistance by backcrossing to V arizonica, while the bottom graphs represent susceptible V. vinifera cutlivars. c. Plots of kmer frequencies in six Vitis species. The species phylogeny is shown on the left, with the average detection frequency of R-kmers shown in red dot. The gray dots represent average detection frequencies of randomly chosen kmers that had similar population frequencies in V. arizonica as the set of R kmers. Whiskers denote 95% confidence intervals.

controlledIPD-YESFeb 2026View details →

ClinicalTrials.gov32/100

Multigene Germline Panel Testing in Gastric Cancer Patients in Portugal

ClinicalTrials.gov study NCT07387237. IPD Sharing: YES. Countries: 1. Publications: 0.

publicSep 2019View details →

Data from: Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family

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publicDec 2017View details →

Data from: A species-specific multigene family mediates differential sperm displacement in Drosophila melanogaster

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publicJan 2014View details →

Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia

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publicApr 2017View details →

Data from: Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance

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dryad28/100

Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs

Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.

opencc-zeroDec 2019View details →

dryad28/100

Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species

The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.

opencc-zeroDec 2012View details →

Figure 9 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 9 Cytospora sorbariae from Sorbaria sorbifolia (BJFC CF20230417) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E, F conidiophores and conidiogenous cells G conidia. Scale bars: 1 mm (A); 100 µm (B–D); 10 µm (E–G).

Figure 8 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 8 Cytospora pinea from Pinus bungeanae (BJFC CF20230413) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E conidiophores and conidiogenous cells F conidia. Scale bars: 2 mm (A); 200 µm (B, D); 100 µm (C); 10 µm (E, F).

Figure 2 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 2 Phylogram of Cytospora based on Maximum Likelihood (ML) analysis of the dataset of combined ITS, act, rpb2, tef1-a and tub2 genes. Numbers above the branches indicate ML bootstrap values (ML-BS ≥ 60%) and Bayesian Posterior Probabilities (BPP ≥ 0.9). Ex-type isolates are in bold. lsolates in this study marked with its hosts and highlighted in two different colours where the novel species are shown in dark blue and the known species are shown in light blue.

Figure 5 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 5 Cytospora euonymina from Salix babylonica (BJFC CF20230403) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E, F conidiophores and conidiogenous cells G conidia. Scale bars: 500 µm (A); 200 µm (B); 100 µm (C, D); 10 µm (E–G).

Figure 4 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 4 Cytospora albodisca from Euonymus japonicus (BJFC CF20230402) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E conidiophores and conidiogenous cells F conidia. Scale bars: 2 mm (A); 1 mm (B); 500 µm (C); 200 µm (D); 10 µm (E, F).

Figure 3 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 3 Cytospora ailanthicola from Salix matsudana (BJFC CF20230400) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E, F conidiophores and conidiogenous cells G conidia. Scale bars: 1 mm (A); 200 µm (B); 100 µm (C, D); 10 µm (E–G)

Figure 6 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 6 Cytospora fengtaiensis from Acer palmatum 'Atropurpureum' (BJFC CF20230405) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E conidiophores and conidiogenous cells F conidia. Scale bars: 1 mm (A); 200 µm (B–D); 10 µm (E, F).

Figure 7 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 7 Cytospora haidianensis from Salix babylonica (BJFC CF20230411) A, B habit of conidiomata on branch C transverse section through conidiomata D longitudinal section through conidiomata E, F conidiophores and conidiogenous cells G conidia. Scale bars: 1 mm (A); 200 µm (B–D); 10 µm (E–G).

Figure 1 from: Jia A, Chen B, Lu H, Xing Y, Li B, Fan X (2024) Multigene phylogeny and morphology reveal three new species of Cytospora isolated from diseased plant branches in Fengtai District, Beijing, China. MycoKeys 101: 163-189. https://doi.org/10.3897/mycokeys.101.116272

Figure 1 Disease symptoms associated with Cytospora species collected from Fengtai District, Beijing, China AAcer palmatum 'Atropurpureum' BAcer pictum subsp. Mono. CEuonymus japonicusDMalus 'American' EMalus × micromalusFPinus bungeanaeGSalix babylonicaHSorbaria sorbifolia.