LIS - Legume Information System Information about legume traits for crop improvement
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Apr 2018 update: new gene families are here; also, multi-genomic macrosynteny in GCV The new gene families at LegumeInfo were calculated as part of the NSF LegumeFederation project, 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: Arabidopsis thaliana, Prunus persica, Cucumis sativa, Solanum lycopersicum, and Vitis vinifera. 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 multiway 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: Expression profile neighbors Microsynteny views (click a gene family in the legend to access the link) Phylogeny views (click an internal node in the tree to access the link for the legume genes in the subtree at that node) 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. Examples: Microsynteny view of Mlo-related protein. Gene page of the same. Search for all Mlo-like cowpea genes. CowpeaMine report page for a different Mlo-like protein (check the overlapping QTL list for this gene). CowpeaMine visualization for genotypes of mapping population CB27_x_IT82E-18. 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. Examples: 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 New genetic map for common bean or via Map Search (map BAT93_x_JALOEEP558_c; Blair et al., 2017), with new GBrowse track of mapped markers. Also see the Blair et al. (2017) map in a genetic-to-physical comparison, using the new CMap-js map viewer, here. New cowpea genome assembly and annotations are ready in the Phytozome "early release" set. Coming soon (est. Oct.) to LIS. 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 Create a list from a publication: A global view of transcriptome dynamics during flower development in chickpea by deep sequencing From the list view: Manage columns, filters or relationships between items on the list Save the list for a later use (only if logged in) Export and download the list View the RNA-seq expression of the list (near the bottom of the page) View the GO Enrichment and Chromosome Distribution of the list (near the bottom of the page)
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 LISmanaged 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 listbased 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.
Sept 2016 update: Narrow-leafed lupin genome browsers, expression atlas data, Glycine trait evaluation data, userfocused 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) 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) 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 It is now possible to upload datasets to the Legume interactive geographic map. See example here. (Data from Lucas et al., 2013) New interactive alignment viewer for gene families - see example family, and alignment viewer at "View Multiple Sequence Alignment (MSA)". Genome viewers (GBrowse, JBrowse) for a desi chickpea, genotype ICC 4958. This extends other chickpea resources in LIS, including browsers for kabuli variety CDC Frontier. Improved QTL search, including searches off-site in other databases. 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 Genome browser for red clover: with annotated gene models (also available via searches for gene function and domain content) and synteny with other cool-season legumes. BLAST targets for red clover genome, CDS and proteins. 12857 new bean SNP markers, e.g. ss715648187. New map: Stampede_x_RedHawk_F2, described in Song, Jia et al., 2015. Germplasm trait evaluation data added from GRIN for: Lens, Lathyrus and Vicia. Posters and presentations from PAG. Multiple sequence alignment display in jalview now includes domain annotations for family consensus. Jan 2016 update: geographic map-based displays of germplasm data, genome context viewer enhancements, LIS in NAR 2016 Database issue GRIN germplasm passport data for all legume taxa and trait evaluation data for six legume genera now viewable in world geographic contexts New interactive tour of genome context viewer features (tour initiated via Help button) Improvements to alignment algorithms for display of inversions and other complex rearrangements in context viewer Please check out our Nucleic Acids Research 2016 Database issue publication and don't forget to cite LIS if you use it for your research! Dec 2015 update: Red clover genome; speedier genome context viewer; new help & FAQ features; improved gene pages New red clover genome sequence available at BBSRC; JBrowse here. Story here. Integration into LIS, coming soon. The services behind the synteny / genome context viewer have been optimized to improve data loading speed. New quick, interactive tour of gene family features. New Frequently Asked Questions (FAQ) section. Improved gene report pages, with more easily accessible sequences, e.g. Glyma.15G026400. Nov 2015 update: Bean markers from many publications have been added; many enhancements to displays of genebased 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 A mungbean (Vigna radiata) genome browser and gene models are now available at LIS. The genome sequencing project, led from the lab of Dr. Suk-Ha Lee, has a home page here. The genome is described in Kang et al., 2014: "Genome sequence of mungbean and insights into evolution within Vigna species". Lotus (Lotus japonicus): LIS now has the latest version of the genome (version 3.0), thanks to the Lotus genome consortium. The previous version (2.5) is also available. The gene models (v3.0) are also listed at the genes search page. Both new gene model sets have been included in the Phytozome 10.2-based gene families and as BLAST-able target databases. Gene trees now come with explanatory legends, see here for example. 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 OziaAkins 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. Gene family memberships and trees have been rebuilt using Phytozome 10.2 family models, and now include chickpea and pigeonpea genes in addition to previously included legume species. Improvements in the "genome context viewer" available from each gene tree. Improvements to map and marker data handling and presentation. QTL data from Asfaw A and Blair MW. (2012) and Asfaw A, Blair MW et al. (2012) now available. Numerous bug fixes. 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. Gene descriptors* have been added for all legume species currently included in the gene trees. These are searchable via the gene search page. Sequence data for transcripts/proteins are accessible via gene search page, through the Sequences tab associated with the genes and their related features - for example, this bean gene. Come visit us at PAG, for the LIS computer demo or stop by the Plant Databases Booth (#407). Legume talks at 2015 PAG Data submission template for QTL, map, and marker data. *(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 Gene tree searches by family characteristics: supports filtering/sorting/display of gene counts, both total and per-species (legume species only) Gene tree searches by gene or family name or description; NB: currently data for gene descriptions in many species is absent, to be added soon 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 Lotus japonicus gene models updated to the version at ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/Lj2.5_gene_models.gff3, which includes previously-missing gene models (click here to view this track). Common bean: new tandem-repeat (centromeric) tracks, pericentromere boundary, synteny tracks - including with soybean assembly v2.0. Medicago: improved synteny tracks. Pigeonpea: new synteny tracks with soybean assembly v2.0. 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
