askPulse

Function of a gene through its Arabidopsis thaliana orthologue(s): Ensembl Plants Compara orthologues, then UniProtKB curated function, protein and gene names, mutant (disruption) phenotype, subcellular location and GO terms. gene: an Ensembl gene ID or name of any crop genome here, or an AGI (AT5G10140) / Arabidopsis name (FLC); in askBrassica also a B. napus pangenome gene (BnaA01g00010.1D2, BnaPanG...). one2many / many2many orthologues are all listed; the crop gene's own function is inferred, not shown.

What askPulse currently indexes: record counts per database and data type, and data versions.

Soybean and Medicago RNA-seq experiments held by askPulse (Expression Atlas and, for chickpea and pea, the Legume Information System): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). query filters descriptions/labels (e.g. 'drought', 'grain', 'Fusarium'). Gives each experiment's assay groups (baseline) or contrasts (differential).

Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text matched to group labels, e.g. 'root', 'grain'): genes with TPM >= min_tpm in a matching group ranked by specificity = (max TPM in matching groups + 1) / (max TPM in other groups + 1). Differential experiment + contrast (text matched to contrast names or IDs): significant genes, direction 'up' or 'down', ranked by |log2FC|. Use expression_experiments() for group and contrast names.

Look up a gene by Ensembl gene ID or gene name/symbol in Ensembl Plants: species, location, assembly, biotype, description and link. Names are searched in all of: pisum_sativum (Cameor v1a), pisum_sativum_gca024323335v2gb (pea ZW6), pisum_sativum_gca964186695v1gb (pea JI2822), vicia_faba, lupinus_angustifolius, phaseolus_vulgaris, cajanus_cajan_gca000340665v2gb (pigeonpea), vigna_unguiculata_gca004118075v2rs (cowpea), vigna_radiata, vigna_angularis, glycine_max, glycine_soja, arachis_hypogaea, medicago_truncatula, trifolium_pratense (red clover) (or only in species, if given). e.g. 'GLYMA_01G000600', 'Psat1g000360'.

Find pulse and legume genebank accessions by accession number or name (e.g. 'ICC 4958' for chickpea at ICRISAT): chickpea, lentil, pea, faba bean, lupin, grass pea, Phaseolus, Vigna, pigeonpea, soybean, peanut and Medicago accessions from GBIF, with the holding genebank (FAO WIEWS code, e.g. IND002 = ICRISAT, SYR002/LBN002 = ICARDA) and accession number; mostly Svalbard safety duplicates. Passport data are minimal (no traits). Also INRAE GnpIS pea and faba bean collections via FAIDARE, with taxon, holding institute, country of origin, status, pedigree and panels.

Where and when a pulse and legume gene is expressed, and under which treatments it changes, from Expression Atlas and, for chickpea and pea, the Legume Information System. gene: Ensembl gene ID (e.g. GLYMA_01G000600, pea Psat1g000360), a chickpea CDC Frontier v3 ID (Ca1g000100) or a gene name find_gene resolves. Baseline: TPM (median over replicates, with range) for the top_groups highest-expressed tissues/stages per experiment. Differential: every contrast where the gene is significant (adjusted p < 0.05, |log2FC| >= 1). experiment restricts to one accession.

Plant Reactome metabolic and signalling pathways of a gene (Gramene), with the top-level category and a link to the pathway diagram. gene: an Ensembl Plants gene ID or a gene name/symbol. Pathways are projected from rice by orthology, so say they are inferred. Use pathway_genes for the reverse (all genes of a pathway).

Genes overlapping a region of one Ensembl Plants genome (max 5 Mb). species is an Ensembl name, e.g. 'pisum_sativum', 'vicia_faba', 'glycine_max' or 'lupinus_angustifolius'; chromosome names as in that assembly. Chromosome names differ by assembly: pea 1LG6..7LG7, narrow-leafed lupin LG01..LG20, soybean 1..20; faba bean uses ENA sequence accessions (e.g. OX451735.1).

Full record for one paper: DOI (10.xxxx/..), PMID (digits) or PMCID (PMC...). Returns the abstract, open-access status and full-text links.

Members of an LIS legume gene family across chickpea, lentil, pea, soybean and Medicago truncatula. gene: a chickpea/lentil/pea/Medicago gene ID, a soybean Ensembl ID (GLYMA_01G000600) or LIS name (Glyma.01G000600), or a family ID (Legume.fam3.00142). Use it to go from a soybean or pea gene (e.g. from orthologues or expression results) to its chickpea and lentil relatives, or back. Families are broader than orthologue groups. dataset (e.g. 'chickpea_desi' or 'chickpea_kabuli_v1') picks one when a Ca_ ID exists in several annotations.

Chickpea or lentil gene from the Legume Information System (these genomes are not in Ensembl Plants): location, functional description, LIS legume gene family and link. gene: a gene ID (e.g. 'Ca1g000100', 'Lcu.2RBY.1g000010') or words from the description (e.g. 'flowering locus T') to list matching genes. Datasets: 'chickpea' = Cicer arietinum CDC Frontier (kabuli) assembly v3 (gene IDs like Ca1g000100, chromosomes chr1-chr8); 'chickpea_kabuli_v1' = the original kabuli CDC Frontier genes (Ca_00001 IDs used in most chickpea papers) placed on the UWA kabuli v2.6.3 assembly (Ca1-Ca8); 'chickpea_desi' = desi ICC 4958 genes (also Ca_ IDs, but different genes from the kabuli Ca_ IDs) on the UWA desi v3.0 assembly (Ca1-Ca8); 'lentil' = Lens culinaris CDC Redberry assembly v2 (IDs like Lcu.2RBY.1g000010, chromosomes Chr1-Chr7). Gene families (LIS legume.fam3) also cover pea (Cameor, Psat... = Ensembl Plants pisum_sativum IDs), soybean (Wm82.a2, Glyma.01G000600 = Ensembl GLYMA_01G000600) and Medicago truncatula (A17 v5, MtrunA17Chr...).

Chickpea or lentil genes in a region (max 5 Mb) with descriptions and gene families. dataset 'chickpea' (CDC Frontier v3, chromosomes chr1-chr8), 'chickpea_kabuli_v1' (UWA kabuli v2.6.3, Ca1-Ca8), 'chickpea_desi' (UWA desi v3.0, Ca1-Ca8) or 'lentil' (Chr1-Chr7). Chromosome numbers alone (e.g. '4') are accepted.

The same gene across chickpea or pea assemblies and annotation versions, from LIS pangene sets (synteny-aware clustering). Chickpea (Cicer.pan3): kabuli CDC Frontier v3 (Ca1g000200), v1/v2 (Ca_00003), desi ICC 4958 (Ca_) and wild C. reticulatum (Cr1g…) and C. echinospermum (Ce…). Pea (Pisum.pan1): Cameor v1a (Psat1g000360 = Ensembl pisum_sativum), Cameor v2 (Psat.1g…), JI2822 (PSAT_LOCUS… = Ensembl JI2822) and ZW6 (Psat01G…). gene: any of these IDs or a pangene ID. Use it to convert IDs between assemblies (e.g. a kabuli Ca_ ID from a paper to the v3 gene with expression data). dataset ('chickpea_desi', 'chickpea_kabuli_v1', ...) disambiguates a shared Ca_ ID.

QTL and GWAS results for legumes from the Legume Information System: soybean (SoyBase QTL on genetic maps plus GWAS; marker positions on Wm82.a2 = Ensembl glycine_max), common bean (G19833 v1 = Ensembl phaseolus_vulgaris; some GWAS on G19833 v2), cowpea (IT97K-499-35 v1) and peanut (Tifrunner v2). Search by trait words (e.g. 'seed oil', 'pod dehiscence'; soybean traits use SoyBase names such as 'SCN', 'SDS', 'Sclero', so check legume_qtl_traits) and/or a physical region (species + chromosome as in the marker assembly or the Ensembl name, start, end). Returns each QTL (genetic map, linkage group, cM interval, markers) or GWAS association (marker, p-value) with study, DOI and marker positions; ensembl_region gives genes_in_region arguments where the markers are on the Ensembl assembly. Chickpea, lentil, pea and faba bean QTL are not in LIS yet.

Traits with QTL or GWAS results in the Legume Information System, with counts per species (soybean (SoyBase QTL on genetic maps plus GWAS; marker positions on Wm82.a2 = Ensembl glycine_max), common bean (G19833 v1 = Ensembl phaseolus_vulgaris; some GWAS on G19833 v2), cowpea (IT97K-499-35 v1) and peanut (Tifrunner v2)). query filters trait names (e.g. 'seed', 'rust').

Narrow-leafed lupin (Lupinus angustifolius) genetic map: 9,972 markers (DArTseq SNP/PAV, Fluidigm SNP, indel, SSR, gene-based) and domestication loci (Tardus and Lentus pod shattering, Leucospermus white flower/seed, Iucundus low alkaloid, Mollis soft seed, Ku vernalisation independence, Lanr1 anthracnose resistance) on the 97L380 RIL map (83A:476 x P27255), with positions on the Tanjil reference (= Ensembl Plants lupinus_angustifolius, LG01-LG20) and Medicago Mt4.0 hits. Search by marker name (exact or prefix), trait words (e.g. 'alkaloid', 'pod shattering'), Tanjil region (chromosome LGxx + start/end) or map interval (chromosome + cm_start/cm_end). For trait loci and unplaced markers the physical interval comes from the nearest anchored map neighbours, with genes_in_region arguments.

Orthologues of a gene from Ensembl Plants Compara (gene trees across plant genomes), e.g. the Brassica copies of an Arabidopsis gene. gene: Ensembl ID or name; target_species: Ensembl name to restrict to (e.g. 'medicago_truncatula' or 'pisum_sativum'). Returns orthologue IDs, species, relationship (one2one, one2many, many2many).

Genes in a Plant Reactome pathway: pathway is a name or words from it ('jasmonic acid biosynthesis', 'gibberellin', 'flavonoid') or a stable ID (R-TAE-1119332). species: a species name as Plant Reactome writes it ('Triticum aestivum', 'Brassica napus', 'Glycine max'); default all species loaded for this site. Matching pathways are listed with their genes per species. Membership is projected from rice by orthology.

Interactive gene view for one pulse and legume gene: a relationship map of its orthologues across legumes (Ensembl Compara), members of its LIS legume gene family (chickpea, lentil, pea, soybean, Medicago), Arabidopsis function, expression contrasts and recent papers, with tabs for the gene family by species and baseline expression (LIS chickpea and pea atlases, Expression Atlas). Clients that support MCP Apps show it in the chat; the result also lists the nodes, the panel data and the gene page link (page) to share. gene: gene name or Ensembl/LIS ID.

Full-text search across all askPulse resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Legume Information System', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping Experiment', 'File'; species e.g. 'Pisum sativum', 'Vicia faba', 'Glycine max'. Returns total count, facet counts and the top hits with source URLs.

Search publications and preprints in Europe PMC (PubMed, PMC, bioRxiv and others). query: free text or Europe PMC syntax (e.g. 'grain size QTL 6A', 'TITLE:"pan-genome"'). gene: optional gene name or Ensembl ID; its curated synonyms and RefSeq IDs are OR-ed into the query (e.g. gene='GLYMA_01G000600'). Words are matched in title and abstract; full_text=True also searches open-access full text. crop_only requires a legume crop or genus name in title or abstract. sort: 'relevance', 'date' (newest first) or 'cited'. Returns hit count and papers with DOI/PMID, year, journal, open-access flag, citations and a short abstract.

Trait-associated positions across the genome for a chromosome overview: GWAS marker-trait associations and peaks, named trait genes and mapped trait loci held by this site, with chromosome sizes, each with a genome browser link where the assembly is loaded. trait: words to match (e.g. 'height', 'oil', 'alkaloid'); chromosome filters one chromosome. Map marker tracks are left out unless a chromosome is given.