Research article
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family
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* Corresponding author: Joel B Dacks dacks@ualberta.ca
1 MOLBINFO unit, Department of Biology, University of Padua, viale G. Colombo, 3 - 35131 Padova, Italy
2 Department of Cell Biology, University of Alberta, 6-30 Medical Sciences Building, Edmonton, Alberta, Canada
BMC Genomics 2009, 10:510 doi:10.1186/1471-2164-10-510
Published: 4 November 2009Additional files
Additional file 1:
Table S1. Accession numbers and names of all sequences identified in our comparative genomic searches and used in phylogenetic analyses.
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Additional file 2:
Table S2. Whole complements of "classic" longins from a number of model plant species.
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Additional file 3:
Alignment of the VAMP727 loop region in diverse plants. This figure shows a multiple alignment of the conserved VAMP727 acidic loop region including a few adjacent C-ter and N-ter residues, corresponding to regions 94-121 or 96-124 of VAMP727 proteins from respectively Arabidopsis thaliana or Oryza sativa. Loops regions are 98-116 (At) and 100-119 (Os) respectively.
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Additional file 4:
Longin phylogeny. This figure demonstrates that the Phytolongins form a well-resolved clade within the longin family and that they are unlikely to have been derived from within the Ykt6 clade of longins. The vertical bars highlight the Ykt6 and Phytolongin (PL) clades respectively.
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Additional file 5:
Phytolongin phylogeny (altered taxon sampling). This figure shows the robust separation of bryophyte and gymno/angiosperm sequences. This dataset included a homologue from Salaginella moellendorffii but excluded a divergent sequence from Sorghum bicolor and resulted in a more robust resolution of the Physcomitrella patens sequences from the other plant Phytolongins (vertical bar).
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Additional file 6:
Table S3. Characteristics of datasets used in phylogenetic analysis. Datasets are listed by name, number of taxa, number of amino acid positions, the model of sequence evolution deduced by Prot-test and the figure in the paper in which the results are illustrated.
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