• Oct 2021 update: tepary bean genomes

    Phaseolus acutifolius (tepary bean) is a drought- and heat-tolerant crop native to the American Southwest and Mexico; it joins the growing set of annotated genomes at LIS, with a cultivated and wild accession described in Moghaddam et al. 2021. The cultivated accession has been added as the primary representative of the species, and can be found via the standard gene search pages, and genome browsers, while the wild species is accessible via a Phaseolus data source for the GCV instance located here, which also includes several new accessions of Phaseolus vulgaris (UI111 and LaborOvalle), courtesy of Phytozome.

  • Feb 2021 update: new genomes for Aeschynomene evenia and Medicago sativa

    Two interesting new genomes have been added to the collection of resources at LIS:

    • Aeschynomene evenia (jointvetch) has been used as a model for study of an unusual form of nodulation present in several members of the genus that is independent of Nod factors and infection threads, forming nodules on both stems and roots with photosynthetic Bradyrhizobia. The annotated genome was recently published by the Arrighi lab, who kindly made it available to LIS prior to publication, and who maintains the primary site for this genus at AeschynomeneBase. If you're curious, why not do a quick search for Nodulins at JointvetchMine?
    • Medicago sativa (alfalfa) is an outcrossing autotetraploid of significant economic importance due to its use as a forage crop. Due to significant levels of heterozygosity including structural variation between the four haplotypes, we imported all 4x8 = 32 chromosomes from the "allele-aware" assembly of cultivar XinJiangDaYe reported by Chen et al. 2020, who used PacBio Circular Consensus Sequencing and Hi-C scaffolding to produce their result for this challenging genome. Note that due to this decision, up to four alleles for any one M. sativa gene may appear in our systems, as can be seen in the GCV view (also showing the types of structural variation present between the homeologous chromosomes).
  • Nov 2020 update: new tools for GWAS, expression, BLAST and Data Store Overviews!

    We're rolling out some new tools that have been in development and updating some others:

    • A new comparative viewer for GWAS and QTL data based on the Baxter Lab's ZBrowse is available for comparing trait-marker associations across multiple species- hence we call it ZZBrowse (example comparing cowpea flowering time QTLs to soybean GWAS)
    • New comparative multi-species views of expression across members of gene families based on the Mutwil Lab's CoNekT; for example, leaf and root preferential expression conserved in Ferredoxin-NADP reductase gene families, accessible from the LIS expression pages of the members of the gene family depicted there.
    • Overviews of data content in views based on Phil Ewel's MultiQC, DSCensorgives users a census of the LIS Data Store, and new ways to compare available genomes and annotations (example of annotations across Medicago truncatula genomes from MtHapMap). And now that the LIS Intermines are built directly from the contents of the Data Store, you can use it to see contents of the files displayed in the overviews by following dataset links in pages such as this one from BeanMine
    • A new look for LIS BLAST services based on Wurm Lab's SequenceServer; we'll plan to phase out the older BLAST services once we're sure the new services meet the community needs as well.

    Questions? Comments? Suggestions? Contact us- we always love to hear your thoughts on how to serve you better.

  • Sep 2020 update: Phaseolus lunatus genome available; release of GCV 2.0 for increased synteny browsing power
    • Early access lima bean (Phaseolus lunatus) genome available:
      The G27455 V1 assembly from Phytozome has now been incorporated into legumeinfo.

      This includes:

    • We're excited to announce the release of a version 2.0 upgrade to our Genome Context Viewer tool, consolidating and extending the functionalities found in the previous version.

      Features include:

      • "Fuzzy search" by gene/region names
      • a user-configurable docking layout-based UI for composition of complex views
      • old "search" and "multi" views have been merged into a single "genes" view combining strengths of both
      • Alerts have been replaced with process pipelines for greater transparency of progression through federated search stages
      • macro tracks can now be ordered and searched, a new micro track clustering algorithm, pervasive use of tooltips for meta data and help text...
      • Major code changes for future extensibility, including a new data model, a new services API,
  • Mar 2020 update: White lupine genome now available

    White lupine (Lupinus albus) genome released:
    The newly published (Hufnagel et al. 2020) Lupinus albus (Amiga) genome produced by the LUPIN ROOT project has now been incorporated into legumeinfo.

    This includes:

  • datastore bulk downloadable versions of genome and annotations;
  • incorporation of annotations into searches from LegumeMine and from the legumeinfo gene search and gene family search;
  • incorporation into the dynamic synteny views provided the Genome Context Viewer;
  • legumeinfo hosted GBrowse/JBrowse and context-specific linkouts to relevant resources within the broader LegumeFederation
  • Jan 2020 update: Mesoamerican bean genome UI111; GCViT genotype explorer tool for chickpea and bean; Comparative GWAS Viewer (ZBrowse)
    • A Mesoamerican bean accession, UI111, is available at the Data Store and for viewing in a genome browser. It can also be compared to other genomes through the Genome Context Viewer, e.g. in this region where the assembly has an inversion relative to the assembly for the Andean G19883 line (but is structurally consistent with corresponding soybean regions). The UI111 line is a pinto-type bean that has been used in numerous breeding projects and trait-mapping studies.
    • A new tool for whole-genome visualization of resequencing or SNP array data, Genotype Comparison Visualization Tool (GCViT), is available for chickpea and common bean. GCViT is useful for comparing two or more accessions, to visually identify regions of similarity and difference across the genome. It extracts information from a VCF file and compares between two or more lines within that VCF file. One can, for example, plot the differences between progeny and parents to identify which regions are inherited from which parents. See more information about GCViT here: a video tutorial, and at GitHub and SoyBase.
    • Several published GWAS datasets are available through a cross-species comparative viewer adapted from the Baxter Lab's ZBrowse. The viewer makes use of comparative genomic services provided by the Genome Context Viewer (GCV) and is intended to facilitate nomination of candidate genes through correlation of variation in orthologous genes with effects on corresponding phenotypes. An example for seed weight in cowpea and soybean based on published data from Lo et al. (2019) and curated data from Soybase is here. Further information about how to get started with ZBrowse is here (and in the interactive tour accessible via "Start tour" link on the main user interface).
  • Oct 2019 update: Pea genome now available

    Pea (Pisum sativum) genome released:
    The newly published (Kreplak et al. 2019) Pisum sativum (Cameor) genome from the Pea Genome Project has now been incorporated into legumeinfo.

    This includes:

  • datastore bulk downloadable versions of genome and annotations;
  • incorporation of annotations into searches from LegumeMine and from the legumeinfo gene search and gene family search;
  • incorporation into the dynamic synteny views provided the Genome Context Viewer;
  • legumeinfo hosted GBrowse/JBrowse and context-specific linkouts to relevant resources within the broader LegumeFederation
  • Aug 2019 update: Latest Medicago genome Mt5.0 and a new tetraploid peanut assembly
    • Mt5.0, the latest Medicago genome:
      The latest version of the Medicago truncatula genome, Mt5.0 has now been incorporated into the legumeinfo datastore: assembly, annotations.
      A full transition to using Mt5.0 in legumeinfo hosted resources is ongoing, but you can see the comparisons of Mt5.0 gene content with the Mt4.0 version (and with other annotated legume genomes) using an instance of the Legume Federation Genome Context Viewer (GCV) here:
      As described in his LegumeFederation blog post, Dr. Nevin Young decided to take GCV out for a test-drive to help answer the question, "Are symbiosis genes, clustered together in the Medicago truncatula genome into so-called ‘symbiotic islands’, also conserved, syntenic and co-linear in the genomes of other legume species?” The study provided insights into symbiotic islands, strengths and limitations of GCV – and also the challenges of comparative genomics based on sequence assemblies coming from diverse sources. More details here:

      Note that clicking on Mt5.0 genes in the GCV will offer links to resources for Mt5.0 developed by the group at the Laboratory of Plant-Microbe Interactions who produced and published this new version of the Jemalong A17 genome assembly (Pecrix, et al. 2018 Nature Plants (4(12) 1017-1025),). The Mt5.0 genome also has a JBrowse instance set up at the http://medicagohapmap2.org site, featuring a plugin developed at JCVI for highlighting features relevant to gene structure in a text display of the sequence (similar to the TAIR “SeqViewer Nucleotide View”). To access this feature, right click a gene and ask to View Sequence. We have heard Medicago users requesting this functionality, and now hope to deploy it to other JBrowses in the Legume Federation family- if it’s something you want to see sooner for your favorite genome let us know!

    • New peanut assembly:
      A new tetraploid peanut assembly (a structural update) along with the corresponding annotations can now be found at the Data Store. This version is essentially the same as Tifrunner version 1 (arahy.Tifrunner.gnm1.KYV3.genome_main.fna) at the base pair level, but has several large structural rearrangements, on the basis of HiC assessments, contributed by the Aiden lab at Baylor College of Medicine. See a summary of the changes here.
  • Mar 2019 update : new GCV features

    The multi-genome Genome Context Viewer (GCV) has some updated features:

    • Ability to search by genomic span, in addition to the search by gene; for example: glyso.PI483463.gnm1.Gs02:100000-400000
    • Toggle "orphan" gene display on or off from the gene family legend
    • Improved tooltips
  • Feb 2019 update: new genomes for synteny views, updates to expression in gene pages, genotype matrix display in Soymine
    • Glycine gene models from Wm82 genome version 4, soybean cultivar Lee and Glycine soja accession PI483463 have been assigned to the legfed_v1_0 gene families and are viewable together with core LIS genomes in the Genome Context Viewer (GCV); for example, this region updated in version 4 of Wm82 and with gene content differences among the Glycine members
    • Gene expression views on gene pages now provide UI for selection of number of nearest profile neighbors or correlation threshold for any r>0.7, allowing customization of view to more or less tightly circumscribed sets of co-expressed genes. Example page to try the UI.
    • Soymine now incorporates genotype data for the U.S. germplasm collection based on the Soy 50K SNP chip; the Genotype matrix display provided for such data in the mines can be seen here. Note that subsets of lines and markers for display can be created through the use of Intermines List management capabilities; an example is provided in the page based on seed weight associations, but you can create your own sets of markers/lines for display using queries such as these templated queries for markers and for lines.

    Any questions/suggestions about the new data or features? Contact us!- we're always happy to hear from you.

  • Sep 2018 update: Mine Template Queries, Genome Context Viewer update, and more

    Site updates

    • LegumeMine and SoyMine have both been provided with a set of helpful templated queries to make it easy to use the power of the mines to ask common questions, such as "Give me all genes from Chromosome X between Y and Z", then use the results in list analyses provided by the Mines such as GO enrichment analysis. If there's a question you'd like to be able to ask but we haven't thought of it, just tell us!
    • The LIS Genome Context Viewer has been updated to provide easier access and helpful introductory information for new users, including a built-in user tour. It's also now much easier for other groups to configure their own instances appropriate to the specifics of their site, for example the version used for Medicago HapMap Data.

    Data updates

    • SoyMine now features GWAS data curated from the literature by the diligent staff of SoyBase.
  • Jun 2018 update: soybean expression atlas; chickpea expression atlas remapped to Kabuli genome
    • The soybean expression atlas (Libault 2010) is now available at LIS as dataset glyma1.
    • cicar2: Chickpea flower development gene expression atlas (ICC4958 *Desi samples mapped to CDCFrontier **Kabuli genome).
      The original cicar1 dataset maps the Desi samples to its own ICC4958 Desi genome.
    • The species page now shows links to expression datasets if available.
  • Apr 2018 update: new gene families are here; also, multi-genomic macrosynteny in GCV
    • A new set of gene families at LegumeInfo were calculated as part of the NSF LegumeFederation project, to better capture characteristics of the legume plant family. See a typical family here, or go to the family query page.
    • The family construction process was designed to capture the early whole-genome duplication where possible - but not to include duplications resulting from the older early-angiosperm genome triplication. The gene trees include 14 diverse papilionoid legume species from sequenced legume genomes. The trees are rooted, where possible, by genes from one or more of five outgroup species: Prunus persica, Cucumis sativa (both in the Fabidae clade), Arabidopsis thaliana (Malvidae), Vitis vinifera (sister to the Fabidae and Malvidae), or Solanum locopersicum (Asterids).
    • You can also access data for the full gene family set here. These were calculated as follows (to be described in more detail in a paper anticipated for late 2018). Clustering was done on the basis of gene pairs filtered for per-species Ks values. These were clustered using Markov clustering. Sequence match scores of each sequence in a family were used to identify outliers, on the basis of score value relative to the median score for the family. Remaining sequences were re-clustered, added to the HMM set. Then all sequences were searched against all HMMs, realigned, re-screened relative to median match score, and finally used to generate alignments and phylogenetic trees (using RAxML). The trees are rooted, when possible, using the closest outgroup from among five outgroup species listed above.
    • Note: These current gene families at LegumeInfo replace (as of May, 2018) an older set of families that were built on the Phytozome 10.2 Angiosperm-level gene family models. The Phytozome-based families are still accessible by direct URL (for researchers who may have referenced particular families). The URL form for such families has the form: /chado_phylotree/phytozome_10_2.59192412
    • The multi-alignment view of the Genome Context Viewer has been updated to support visualization of multi-way macrosynteny between the chromosomes from which microsyntenic segments were taken. A fuller description of the new functionality can be found here
  • Mar 2018 update: LIS expression viewer enhancements

    This LIS release includes numerous enhancements to for gene expression views. Expression views are currently available for pigeonpea, chickpea, common bean, and cowpea.

    • Gene expression views are visible for genes (e.g. cajca.C.cajan_07765) or via a new Gene Expression Summary Page.
    • The expression viewer's navigation bar (top gray bar on an expression page; bean example)
      allows switching between four views:
      - Expression for a given gene,
      - Expression for profile neighbors (genes with similar expression),
      - Expression of gene family members, and
      - Information about the expression data and underlying experiments (Dataset Details).
    • Cowpea now has an expression atlas, for the reference genotype IT97K-499-35.
  • Feb 2018 update: macro-synteny extensions for GCV; BLAST from the Mines
    • The Genome Context Viewer has been enhanced to compute macrosyntenic relationships between the query chromosome and other chromosomes in LIS using a dynamic algorithm inspired by MCScanX and based on gene family assignments. The algorithm is user parameterizable and capable of application across federated genomic databases. As a user of LIS GCV, you will no longer be restricted to seeing the pairwise relationships that were pre-computed for the standard genome browsers (e.g. compare synteny blocks available for cowpea dynamically constructed here against those precomputed here. See the Legume Federation site for examples working across LIS and some of its federated partners.
    • The LIS InterMines are now able to communicate with LIS BLAST services. Just click on the BLAST links in any list of features to send the sequence underlying the feature to BLAST against one of the LIS-maintained BLAST target databases. For example, if you're interested in the conservation of a region upstream of an annotated gene in a related genome, scroll down to the Flanking Regions section of the gene report page (e.g. for this diploid peanut gene) and follow the BLAST link to get started.
  • Dec 2017 update: empowered by LegumeMine, and Pigeonpea Expression Atlas
    • LegumeMinenow contains genomic data for all species with genomes in LIS. This enables some powerful features such as gene set enrichment analysis and bulk downloads in a variety of formats to be easily accessible to LIS users through new list-making links available in key locations throughout the legumeinfo site.
      Try your hand at LegumeMine list-making in any of these places:
    • New expression dataset:
      "Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation"
      Pazhamala et al. (2017)
      See, for example, this floral development transcription factor and try making a LegumeMine list from the link provided with the Profile Neighbors plot to assess Gene Ontology enrichment and other aspects of the set.
  • Nov 2017 update: browser for common bean v2.0 assembly, major enhancements to Genome Context Viewer and CMap-js
    • New genome browser for common bean assembly v2.0 (Phaseolus vulgaris G19833). The v1.0 assembly will remain available, but we will gradually transition to using v2.0 for default displays and data sources.
    • New CMap-js features - for example, view the two bean assemblies (v1.0 and v2.0) in CMap-js.
    • Major enhancements to the LIS Genome Context Viewer (GCV) including greatly improved application load times and new multiple alignment capability, allowing you to take a set of genes (such as those belonging to a complex gene family), cluster the genomic contexts in which they appear based on the similarity of thier gene content and produce multiple alignments for each group based on inferred Profile Hidden Markov Models; this can be used by requesting the multiview for the set of genes in a family brought together in a search view, or by requesting the multiview associated with an internal node of a gene tree, which will collect contexts associated with the leaves of the subtree at the node and perform the requested analysis. Here is an example, based on the set of genes from an F-box/LRR family.
  • Sep 2017 update: cowpea genome live at LIS; enhancements to expression data
    • Thanks to close collaboration with cowpea researchers at UC Riverside, the Vigna unguiculata genome and annotations recently released in Phytozome are now available through the browsing and search interfaces in LIS, subject to the same data release policies described here. Genomic and genetic data for cowpea have also been made available through the newly released CowpeaMine.
    • Management and display of expression data has been enhanced with new visualizations in gene pages for displaying
      expression of genes from the same gene family and for displaying the expression of genes with similar expression profiles.
      1. A chickpea gene predominantly expressed in the reproductive tissues and another predominantly in the vegetative tissues with a family member also showing a similar expression profile.

      2. Flower-specific expression of a peroxidase super family gene in common bean and another one predominantly expressed in the root.

  • Aug 2017 update: new bean map and browser tracks; first use of CMap-js viewer; new cowpea genome
  • May 2017 update: Genome Context View (GCV) updates and New ChickpeaMine

    A goal of the LIS and LegumeFederation team is to create resources for legume research and advancement of legume trait improvement. One resource we updated recently is the Genome Context Viewer (GCV), which visualizes regions of genomes considered primarily with respect to the ordering and orientation of their annotated genes. Medicago truncatula Genome Database (MTGD), a Legume Federation genomic data portal (GDP), added links to the Medicago genes presented in the Genome Context Viewer and the LIS gene family phylogram. By clicking on any Medicago genes you can view the links for MedicMine, MTGD gene page and MTGD JBrowse.
    Other updates to the GCV include:

    • Inclusion of full set of tracks with macrosyntenic relationships to query track; those chromosomes having synteny to the region displayed in the microsynteny view are still featured at the top of the display, ordered in accordance with the microsynteny track ordering
    • Color legend for species in macrosynteny (consistent with taxon coloring scheme used in our phylotree and GIS views)
    • Shading of backgrounds to help differentiate between chromosomes
    • Resizable split pane dividers between the macrosynteny or microsynteny panes and their respective legends

    Legume Federation and LIS have released a new Legume Mine: ChickpeaMine. This version of ChickpeaMine contains the same two chickpea genomes that are available on LIS. Chickpea desi (version ICC4958 v2.0) and chickpea kabuli (version CDC Frontier v1.0). Here are some examples on how use the ChickpeaMine and other Mines:

    • Example: Search and Create list
      • Use the keyword search box to search for a gene, ID or keyword Example Search: seed protein
      • Use the Categories box on the left side to sort through the search results Example: Hits by Category Gene
      • Create list from sorted search results by first selecting the genes you want in your list, then clicking on the "create list" button
    • Example: Gene Expression

    The LIS and Legume Federation team will continue to add more data and resources. Check the LIS and Legume Federation websites for more updates.

  • Apr 2017 update: new service for adding user sequences to LIS gene family trees, powered by LegumeFederation "lorax" services

    The protocol used for constructing alignments and trees for the gene families in LIS has been developed into a service to enable users to submit their own sequences to be added to the trees for these families.

    Through the previously released functional annotation tool, gene family assignments are made using HMMER to find the best gene family match out of the subset of phytozome 10.2 Angiosperm gene family models for which LIS-managed genomes have one or more members. These gene family assignments are listed in the table of annotations for the sequences. To initiate the computation of multiple sequence alignments (MSA) and phylogenetic trees for a family, click on the "tools" icon next to the gene family link in the table. This will include all the user submitted sequences assigned to the given family in a single execution of the services, resulting in a view of the gene family phylogeny that is based on the standard LIS phylotree view (including access to the underlying MSA). More details on the services underlying this feature can be found in the lorax code repository.

    Note that we have imposed an initial maximum time limit of 15 minutes for the tree calculation- this may be insufficient to enable construction of trees for very large families. Future releases of the tool will work to relax this restriction.

    Other enhancements to the annotation tool include making InterPro analyses optional for faster lightweight annotation, the inclusion of more information in the summary table and the use of DataTables to enable sorting and filtering of the summary information.

  • Feb 2017 update: functional annotation service, Genome Context Viewer enhancements, Phaseolus vulgaris expression data
    • A new service for annotating user-supplied protein or transcript sequences with Automated Human Readable Descriptions (AHRD) based on functionally-oriented homology searching and lexical analysis is available here. This service is based on the same protocol used to produce descriptions for gene annotations for genomes managed in LIS, and includes tentative assignments of the user sequences to the LIS gene families.
    • The Genome Context Viewer (GCV) has been enhanced with several user-requested features, including:
      • Ability to navigate to new regions of the query chromosome by dragging the focus indicator in the macrosynteny track.
      • High-quality image and data downloads for views in the GCV now available by right-clicking on any of its graphical views.
    • RNA-seq gene expression atlas data for Phaseolus vulgaris is now available as profiles based on TPM (transcripts per million) quantification within individual gene pages (ex: a stress response gene very highly expressed in root tissues).
  • Jan 2017 update: Data Store, new genomic BLAST hits overview, expression viewer, enhanced user interface for multi-genomic synteny
    • New Data Store, for bulk data (genomes, annotations, etc.)
    • New interactive, whole-genome overview of BLAST searches against genomes, with nucleotide-nucleotide or protein-nucleotide searches against single genomes
    • Expression profiles from a flower development atlas dataset added for chickpea genes (both desi and kabuli), e.g., this disease resistance protein from the desi genome (ICC4958), cicar.ICC4958.Ca_08817 and its ortholog in the kabuli genome (CDCFrontier), Ca_10861_gene. (The expression profile feature shown here implements the 'Tripal Analysis Expression Extension Module' developed by Meg Staton's group at the University of Tennessee)
    • The LIS Genome Context Viewer has undergone a major refactoring to enhance performance, ease of use and coordination among the various components of the display; to explore the new interface, take the updated tour!
  • Nov 2016 update: dynamic user-interaction features added to gene family displays, transcription regulation analysis tools added to mines
    • The phylotree and multiple sequence alignment component associated with the gene families have been upgraded to provide significantly more control over coordinated display of subsets of genes of interest, which we hope will help users tailor the displays for the specific questions they are asking, especially with respect to very large gene families and as the number of species included in the families continues to grow. For example, by interacting with the list of species displayed in the legend, one can choose to restrict the tree and alignment to show only members from a subset of species; similarly, the clicking on internal nodes of the trees now provides options to focus in on the subtree rooted at that node, or to collapse and hide the subtree at the node. Other sorts of inter-component interactions are also provided, such as the ability to select sequences from the alignment and see the corresponding nodes in the tree highlighted. You can try these new features out now on this family and click on the Gene Family Help to get access to an interactive tour.
    • The LIS InterMines for soybean, common bean and peanut have been updated with several new features, including
      • Genetic map displays
      • Expression heat maps now available directly from gene lists.
      • Explicit representation of up/downstream flanking regions of genes and introns, with associated list-based analyses for shared motifs

      If you have thoughts on other analyses of this sort that would be useful for us to incorporate, feel free to contact us and give suggestions.

  • Oct 2016 update: enhancements for Genome Context Viewer; functional annotation for narrow-leafed lupin; chickpea flower development atlas
    • The chromosome-scale synteny blocks previously available through the genome browsers have been incorporated into the Genome Context Viewer, in order to provide further information regarding the extent of the macrosynteny contexts in which the microsyntenic gene blocks are located. As in this example, given any pair of sequences (chromosomes or scaffolds) for which macrosynteny has been precalculated (whether between genomes or within a genome), when the context viewer finds a microsyntenic relationship between these sequences, it will now display the complete extent of macrosynteny between the query and target in a new overview pane. Note that not all pairs of genomes have had macrosynteny precalculated, and the methods used for macrosynteny and microsynteny determination will not always agree in all details.
    • Narrow-leafed lupin gene annotations have been functionally annotated, and assigned to LIS gene families (though they will not appear in the gene trees). This enables their inclusion in gene searches, domain searches, and context viewing. The genome browsers have been updated with these functional annotations as well, and the Lupinus angustifolius macrosynteny blocks added in to the context viewer.
    • Chickpea flower development atlas tracks both in Desi (GBrowse, JBrowse) and Kabuli (GBrowse, JBrowse) genome browsers.
      (Singh VK, Garg R, Jain M. A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol J 2013 Aug;11(6):691-701)
  • Sept 2016 update: Narrow-leafed lupin genome browsers, expression atlas data, Glycine trait evaluation data, user-focused site tours
    • Narrow-leafed lupin genome (Lupinus angustifolius) available in browsers (GBrowse, JBrowse)
    • Expression atlas data available from mines for common bean, soybean and peanut; quantitative data based on RNA-seq experiments across a variety of tissues and developmental stages can be queried or displayed in interactive heatmaps for arbitrarily selected lists of mRNA (as in the templated query example Genes => GOTerms => mRNAs)
    • Glycine germplasm trait evaluation data available in map displays, as shown here for chlorosis
    • New site tours available from the Help page
    • Atlas expression tracks for P. vulgaris browsers (GBrowse, JBrowse)
  • July 2016 update: Enhancements to Legume InterMines and Genome Context Viewer through Federation

    For this month, the focus is on enhanced comparative functionality within and outside the legumes
    by means of our partnerships in the Legume Federation.

    Our InterMines now use the "friendly mine" capabilities of Intermine to interlink our own mines together with
    one another and with mines maintained by other groups; e.g. ThaleMine, for a wealth of information
    on Arabidopsis thaliana orthologs to the legume genes maintained in our mines. For those species
    currently stored in the mines (Medicago truncatula, Glycine max, Phaseolus vulgaris, and the diploid Arachis species),
    their LegumeMine gene pages are now directly accessible from the link menus in our phylogenetic trees and our genome
    context views. For example, try going to this tree and click on the highlighted gene from "phavu" (common bean).
    Choose the LegumeMine link in the menu that appears and then look through the details integrated into the report page,
    including the spanning QTLs of the gene. Then check the "Links to other Mines" on the right hand side for further
    information about the orthologs.

    Our Genome Context app now serves genomic data to federated versions of the viewer. A federated viewer
    consuming this service, and supplying data for selected outgroup species (currently Arabidopsis
    thaliana, and four non-legumes from the Fabidae) is now hosted by the Legume Federation, allowing
    exploration of syntenic relationships across longer evolutionary distances. For example, this set
    using Arabidopsis as the query track (note the segmental duplication present in Arabidopsis chromosome 5).
    If you're interested in hosting your own genomes and providing services that can be federated with others
    like ours, check out the Genome Context Viewer code repository
    and contact us if you need any assistance getting started.

  • June 2016 update: New query tool (InterMine); BioProject search for legumes at NCBI; more genomes with gene family assignments; newsletter
    • A powerful new interface (InterMine) deployed to enable querying genomic and genetic data for several legume species - currently, for common bean, soybean, peanut, and a combined LegumeMine for these species (also see the Medicago truncatula MedicMine at collaborating institution JCVI). Developed in collaboration with the NSF-supported Legume Federation project.
    • New search page for BioProjects at NCBI for legume species (accessed from the Search menu).
    • Assignments to gene families for annotations recently-added genomes: Adzuki bean, red clover, chickpea (desi). Note that these do not yet appear in the gene family trees, but are fully usable in gene searches and can have their membership counts displayed in gene family searches. The assignment to gene families also allows these genomes to be used in synteny-based searching, for example: take a gene family, then pick a gene and click on "Find similar genomic contexts for GENE." Example (see regions marked "tripr" and "vigan" for Trifolium pratense and Vigna angularis, and mouseover the "cicar" scaffold to see the gene labels characteristic of the ICC4958 "desi" chickpea).
    • Newsletter sign-up (for our new ~quarterly newsletter; first issue in June, 2016)
  • May 2016 update: Upload data to geographic map; gene family alignment viewer; Desi chickpea; improved QTL search
  • Apr 2016 update: Incorporation of user-supplied germplasm data in maps, utilities for finding recent legume publications
    • The germplasm mapping tool now allows users to upload their own germplasm and observation data for visualization in the context the geographic information framework (see "Add my data" under the Menu options). In addition, a new observation category has been added to enable the display of population structure Q matrices (or other forms of breakdown into proportional composition across a set of categories).
    • A utility to scan the recent literature for legume species at Pubmed.
    • A new citation/reference for LIS and lists of citing articles.
    • Enhancement to the gene linkout popups from our phylotrees, including the ability to traverse directly to our own gene pages. For example, try clicking the leaf node for the highlighted gene here
    • The search gene used in genome context viewer synteny displays now highlighted for ease of interpretation. For example, here
  • Mar 2016 update: Adzuki genome browser and BLAST targets; links from browser to genic synteny views and gene families
    • Adzuki genome (Vigna angularis) available in browsers (GBrowse, JBrowse)
    • Genic synteny views (context viewer) and gene families are now linked from gene models in GBrowse. Click on the gene name for that species and choose Synteny at LIS context viewer page or Gene family at LIS phylotree page.
    • More complete macro-scale synteny information in GBrowse ("from" and "target" synteny coordinates are shown in pop-up boxes for clicked synteny tracks).
  • Feb 2016 update: Red clover genome browser and BLAST targets; new bean markers and map; new genera with trait evaluation data; new outreach material; protein domains in MSA views
  • Jan 2016 update: geographic map-based displays of germplasm data, genome context viewer enhancements, LIS in NAR 2016 Database issue
  • Dec 2015 update: Red clover genome; speedier genome context viewer; new help & FAQ features; improved gene pages
  • Nov 2015 update: Bean markers from many publications have been added; many enhancements to displays of gene-based synteny and phylogeny perspectives
    • More than 9,900 common bean markers have been added to the database from 15 publications.
      See the marker search page, and examples: BM138 , 11M-Gm, BMb318
    • Improved genomic context views and gene tree features and interactivity enhance our users' access to the complementary insights provided by synteny and phylogeny perspectives.

      An example gene tree with bean "Fin" gene (Tfl1 ortholog) highlighted, and a corresponding synteny/genome context view (displaying segments of genomes with similar gene content to that surrounding "Fin"). Returning to the same gene family tree from the context view highlights the syntenic members of the gene family (according to the criteria for synteny defined in the search parameters of the context view).
      User interface improvements include: layout redesign for enabling display of wider contexts; helper bar indicates result of track retrieval and alignment services; dotplots synchronized with ordering and filtering of alignment views; and much more...

  • Oct 2015 update: Improvement in usability of the phylotree view; Germplasm evaluation data for chickpea and peanut
    • Improved usability of the phylotree view:
      We continue to improve the user interface to the phylogenetic tree display for gene families; links to the trees from the gene pages will now highlight and scroll directly to the gene referenced, for example Aradu.6RF6E. User help documentation has been added to all the pages associated with the tree displays. In addition, the genomic context views now have user help documentation accessible from its pages.
    • Trait evaluation data for legume germplasm:
      LIS has begun serving the germplasm evaluation data (for common crop traits or descriptors) for legumes. Data is now available for two legumes, chickpea and peanut. The evaluation data sets have been downloaded from the USDA GRIN website and are served here by LIS. Plans for this feature include improved search capability, and data for more legumes. We request our user community to suggest improvements to make this utility more useful.
  • Sept 2015 update: New Mungbean genome browser and gene information; Lotus genome version 3.0 now at LIS
  • Aug 2015 update: Gene family associations with protein domains; Searches for similar gene contexts; New 'Help' section; Improved cross-browser compatibility
    • Associations of gene families with protein domains.
      Consensus sequences for gene families have been annotated via InterProScan, and the gene families can now be searched in terms of their conserved domain composition:
      • with links (column: Family Count) from the domain search page to the families in which they appear in the consensus
      • via the "Domains/Interpro terms for family consensus" search filter of the gene family search page
    • Searches for similar gene contexts.
      The ability to search for genomic contexts centered around specific genes of interest can be accessed via the gene tree displays; clicking on a legume leaf node will give the option in a popup menu, allowing users to find other genomic regions similar to the one containing the query gene, for example the context surrounding Glyma.14G192500.
    • New 'Help' section: The 'Help' tab now takes you to the 'Site Overview & Guide' page. A work in progress, your feedback on this will help us improve our ability to help all our users with good documentation
    • Improved cross-browser compatibility: The website now properly displays the menu structure in Internet Explorer. Thanks to those who reported the issue to us!
  • Jul 2015 update: Sequence viewer in JBrowse; peanut gene expression atlas; improved context viewer
    • The JBrowse genome viewers (available genomes) have a new sequence viewer plug-in, with the ability to grab up- and down-stream sequence retrieval or reverse-complement sequence around features. Right-click or control-click on any feature (except for synteny), then choose "Sequence Viewer". Also check the new fullscreen viewing capability of this browser ("Fullscreen" button at the top right corner of the JBrowse menu bar).
    • A gene expression atlas with 22 tissues from peanut is now available in the GBrowse genome browsers at PeanutBase, for genomes A. duranensis and A. ipaensis. This pre-publication data is courtesy of Peggy Ozia-Akins lab in collaboration with Brian Scheffler. Transcript densities of these Arachis hypogaea tissues have been mapped onto the combined A. duranensis and A. ipaensis genomes by Wei Huang. Please contact the authors before using or citing this data.
    • The gene family context viewer has been improved: inversions are displayed more clearly, tracks are sortable by chromosome name and distance from the query (alignment score), and it is possible to scroll along the synteny tracks.
  • Jun 2015 update: InterPro domain descriptions for all proteins; improvements to genome context alignment; gene family sequence alignment viewer; new JBrowse bookmark feature
    • InterPro protein domains: The legume gene models have now been annotated with protein domains derived from our InterproScan analysis. You can now search by protein domain IDs or descriptor terms for the associated gene models and gene families in our database.
    • The genome context display now supports a new alignment algorithm specially designed for handling inverted and duplication segments; dotplot visualizations have now been fully integrated into the search display options.
    • Gene family multiple sequence alignments: at a gene family tree view, click the basal node (gray) to download or to view alignment using JalView (needs Java support).
    • New JBrowse feature: save sets of bookmarks (of tracksets and views) under Tools:"Quick Bookmarks"
  • May 2015 update: Phytozome 10.2 gene models, map and marker data improvements, 2 new QTL datasets loaded.
  • Apr 2015 update: View genomes via the faster JBrowse; BLAST hit visualization and Interactive CMap; new gene families
    • Browse the genomes via the faster JBrowse, e.g. chickpea or common bean, or via the genomes page.
    • New BLAST hit visualization, showing the location of hits on the target
    • Access the genetic maps (QTLs too) via the Interactive CMap tool
    • Gene families are available as BLAST targets blastx and blastp
  • Feb 2015 update: Chickpea/Pigeonpea genes loaded, new Gene "basket" functionality, Peanut assemblies in GenBank
    • Gene annotations for chickpea and pigeonpea genome assemblies have been loaded and gene descriptors assigned using Automated Assignment of Human Readable Descriptions (AHRD). PLEASE NOTE: these gene models have not yet been assigned to gene families.
    • Gene "basket" functionality: in the results of a Gene search you will now have the option to add individual rows or the entire query result into a "basket" for applying batch-oriented operations on the basket page. Currently, this supports download of mRNA or polypeptide sequences for the genes. Note that the contents of baskets are session-specific and should not be relied upon for persistent storage of sets. As an alternative, gene lists stored locally may be used as input to a Gene search using the "Contains any word" operator and the gene name list.
    • Genome assemblies of the two diploid progenitors of peanut, A. duranensis and A. ipaensis, were submitted to GenBank and now they have been published.
  • Jan 2015 update: gene descriptors, sequence data added for all species. Activities at PAG. New QTL template.

    *(Descriptor method: using the Automated Assignment of Human Readable Descriptions (AHRD), based on InterProScan results and blastp matches to several annotation sets.)

  • Dec 2014 update: gene tree searching enhancements, gene search
  • Nov 2014 update: New gene family and gene tree feature, new sequence sequence and keyword search utilities, ...
  • New legume-focused gene families and gene trees. There are approximately 13,000 such families with legume sequences (from Glycine max, Medicago truncatula, Phaseolus vulgaris, Arachis duranensis, and Arachis ipaensis). These are based on and extend the Phytozome gene families, and link to the associated gene family resources at Phytozome.
  • A new keyword search utility has been added to facilitate searching for sequence features, such as gene IDs/names, words in annotation, etc.
  • A new BLAST module, with several download formats for download or interactive exploration. All genome searches have links from the blast hits to the respective genome browsers
  • Navigational improvements (we hope you like the home-page changes). Please let us know if you have questions or suggestions.
  • Oct.-Sept. updates: New site design and architecture. New QTL content for common bean, and map and publication searches.

    Design and architectural changes, with switch from Tripal1 to Tripal2.
    New QTL content for common bean, with 9 papers and 275 QTL features (under "Search" tab). Mapped features here on the Galeano et al. 2011 consensus map.
    Keyword search or browsing for QTLs, publications, and maps.

  • First Tuesday of July update: GBrowse enhancements for Lotus, BLAT alignments, new browsers, and more!
    • The BAC clones track in the Lotus japonicus GBrowse previously used SSR names for some of the TACs/BACs; this has been fixed. In addition, the "Lj0" pseudomolecule, which contains contigs that were not placed in the Lj1..Lj6 chromosomes, has been added, and all DFCI transcript & cross-species gene features re-mapped. The JCVI transcripts have been phased-out.
    • Updated list of legume genome browsers at the genomes tab, including two new peanut genomes at the affiliated PeanutBase.
    • Sequence search feature is now available in GBrowse via the BLAT utility.
      The steps for BLAT alignment are (at the GBrowse page):

      1. Select "Find Blat Alignment" in the drop-down menu for Configure.
      2. Click "Configure"
      3. In the "Find Blat Alignment" section that opens, enter your
      (single) sequence in the "Input Sequence to Align" box
      4. Click "Find"

      If a single hit is found, a new track called "BLAT" will be created in the genome browser with your aligned sequence. If multiple hits are found, you'll have to select one from a list of locations.

      If you have questions or need further assistance please contact us.

  • May-June updates: New genome browser features for common bean, Lotus, Medicago, pigeonpea
  • QTLs, Stocks and Markers for Phaseolus are now here

    We have just finished adding 263 QTL features to the common bean data set. With this the database now houses more than 9,000 genetic markers in addition to a list of 26 stocks (cultivars and mapping populations).
    Go to Data Type Summary under Resources in the Phaseolus vulgaris.

    Explore the Phaseolus Stocks
    Search the Genetic Markers
    Search the QTL

  • Legumes at PAG XXII

    Workshop: Legumes
    Sunday, January 12, 2014
    Organizers: Maria J. Monteros and Robert Stupar

    Workshop: Cool Season Legumes
    Saturday, January 11, 2014
    Organizer: Rebecca McGee

  • Meeting: Bean Improvement Cooperative (BIC/NAPIA)

    Bean Improvement Cooperative (BIC/NAPIA)
    Oct 28-30, 2013
    Portland, OR

  • Meeting: North American Pulse Improvement Association (BIC/NAPIA)

    Oct 31 - Nov 01, 2013
    North American Pulse Improvement Association
    NAPIA 2013 Biennial Meeting
    Wednesday, October 30, 2013 at 8:00 AM - Friday, November 1, 2013 at 5:00 PM
    Portland, OR