• 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