gene snp geneview data base  (Biotechnology Information)

Journal: bioRxiv

Article Title: Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

doi: 10.1101/2025.06.16.659998

Figure Lengend Snippet: Determining how and if hosts can choose helpful partners remains an essential but elusive question in mutualism research (Porter et. al, 2024). Here, we examine host genetic variation in selectivity in 202 accessions of Medicago truncatula and then focus on assessing the two hosts’ ability to adaptively enrich the fitness of beneficial strains by increasing the size of nodules and, thus, the population size of those strains.

Article Snippet: We obtained the SNP data for Medicago truncatula A17 from the Legume Information System (legumeinfo.org, ( ).

Techniques:

Journal: bioRxiv

Article Title: Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

doi: 10.1101/2025.06.16.659998

Figure Lengend Snippet: For 202 accessions of Medicago truncatula, we calculated a novel host selectivity by controlling for nodule number differences among plants (a) and quantified nodule morphology variation in nodule pools (16 trait means are visualized here with an RDA). We used LASSO regression with λ = 0.0104 and determined the mean length of the major axis of nodules to be most strongly associated ( p = 4.2 × 10 -6 , adj. R 2 = 0.11) with host selectivity (c). Lastly, we used GWAS to identify host candidate genes associated with host selectivity (Table S2).

Article Snippet: We obtained the SNP data for Medicago truncatula A17 from the Legume Information System (legumeinfo.org, ( ).

Techniques:

Journal: bioRxiv

Article Title: Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

doi: 10.1101/2025.06.16.659998

Figure Lengend Snippet: a) Examples of single replicates of large and small nodule pools from our two host genotypes. (b-e) Nodule Characteristics (weight, length, lobes, colony forming units) of small and large nodules from A17 and R108 hosts. Each data point represents a replicate. The average weight per nodule is based on the fresh weight of the entire pool of nodules, and colony data is the average of replicate dilutions from haphazardly selected nodules from each class. All traits are on a log10 scale. All traits differed (p<0.05) between hosts and nodule size classes based on linear regressions and ANOVA (Table S3).

Article Snippet: We obtained the SNP data for Medicago truncatula A17 from the Legume Information System (legumeinfo.org, ( ).

Techniques:

Journal: bioRxiv

Article Title: Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

doi: 10.1101/2025.06.16.659998

Figure Lengend Snippet: a) Redundancy analysis (RDA) of strain fitness in large and small nodule pools in A17 and R108 revealed that host, size, and their interaction account for approximately 41% of the variation in strain communities. The interaction between host and size ( p <.001, df=1) indicated that hosts enriched different strains in larger nodules. Note that constrained axis RDA 1, which differentiates large and small A17 nodules, explains 4-5 times more variation than constrained axis 2. b) The predicted benefit of the rhizobia found in nodules differs between hosts and nodule size ( p =0.024, df=1). The predicted benefit is estimated by multiplying each strain’s benefit to hosts in a single-strain experiment by its frequency in the nodule pool and summing this across all strains. Since hosts vary in overall size, this sum is scaled such that one represents a nodule community composed entirely of the most beneficial strain, while zero signifies a community composed of the least beneficial strain. c) The relationship between the rewards rhizobia receive and the benefit those strains provide to plant hosts A17 and R108 during single-strain inoculations. The rewards received are measured by their proportional representation in large nodule pools versus the total representation in large and small pools. Each dot represents the median strain proportion across six replicate pots. Single strain plant benefit predicted the enrichment of a strain in larger nodules for both hosts but explained more variation in A17 (34%) than in R108 (15%). Benefits for b and c were estimated by measuring plant biomass in a single-strain inoculation experiment under nitrogen-free conditions (See Tables S4-S6 for complete statistical results).

Article Snippet: We obtained the SNP data for Medicago truncatula A17 from the Legume Information System (legumeinfo.org, ( ).

Techniques:

Journal: Cell Reports Medicine

Article Title: Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

doi: 10.1016/j.xcrm.2025.102143

Figure Lengend Snippet: Clinical characteristics and germline variants associated with NPC subtypes ( n = 303 [L], 201 [A], 246 [D], and 244 [AD]) (A) Representative MRI scans of each NPC subtype (red, bulky tumor; blue, small tumor). (B) CONSORT diagram of patient selection for the NCCS cohort. (C) Association of NPC subtypes with OS and DFS. (D) Manhattan plot showing p values of germline variants associated with L, A, D, or AD subtype relative to healthy controls. Points above dashed line ( p = 8.9 × 10 −7 ) are significant variants post-Bonferroni adjustment. (E) Variants significantly associated with NPC subtypes identified in both the comparison against healthy controls and the comparison against all controls. (F and G) Tumor expression of FADS1 and DFS in A-subtype patients with CC vs. TC genotype of rs72643557 , respectively. The boxplots represent the IQR, with the horizontal line indicating the median. Mann-Whitney U test and log-rank test was used to compare between CC vs. TC in (F) and (G), respectively. Abbreviations: NPC, nasopharyngeal carcinoma; CONSORT, Consolidated Standards of Reporting Trials; QC, quality control; OS, overall survival; DFS, disease-free survival; L, limited; A, ascending; D, descending; AD, ascending-descending.

Article Snippet: The following data files have been made publicly available in Mendeley Data: https://data.mendeley.com/datasets/87cwzd56kh/1 for all analyzed patients: (1) clinical annotation of the NPC subtypes, (2) PLINK files containing genotype data of germline SNPs, (3) MAF files listing detected somatic mutations, and (4) TSV files containing raw gene expression counts and transcripts per million (TPM).

Techniques: Selection, Comparison, Expressing, MANN-WHITNEY, Control