Explanation of alignment files

 

The alignment files are in interleaved PHYLIP format, and can be viewed in a text editor, word processor, or various sequence analysis packages (e.g. BioEdit) that accommodate PHYLIP format.

 

IAAAtOnly.phy – an alignment of the translated sequences from the 28 Aux/IAA sequences from Arabidopsis thaliana, obtained from GenBank.

 

IAAAtOnlyConsRegions.phy – the same alignment as the previous file, but regions that are not well conserved in individual Aux/IAA subgroups have been trimmed.  The tree in Figure 1 of the Remington et al. manuscript was derived from this alignment.

 

IAAAllSpecies.phy – a comprehensive alignment of the translated A. thaliana Aux/IAA sequences, plus sequences obtained from Medicago truncatula, Oryza sativa (rice), Pinus pinaster, and Physcomitrella patens.  Alignments between the A. thaliana sequences are different in some cases from those in the two previous files.  Some apparent errors in sequences from expressed sequence tags (ESTs) have been corrected to obtain more probable reading frames.

 

IAAAllSpeciesConsRegions.phy – the same alignment as the previous file, but regions that are not well conserved in individual Aux/IAA subgroups have been trimmed.  This is one of the three alignments from which the consensus tree in Figure 6 was constructed.

 

IAAAtOnlyConsRegionsAlt.phy – an alternate alignment of conserved regions of the A. thaliana Aux/IAA loci, identical to the above alignment but consisting of only the A. thaliana sequences.

 

ARFAt.phy – an alignment of the translated sequences from the 23 A. thaliana ARF loci, plus a mtDNA fragment showing strong ARF similarity.  Some annotations have been modified by Tom Guilfoyle from those in GenBank.

 

ARFAtConsRegions.phy – the same alignment as the previous file, but containing only the conserved regions.  The tree in Figure 5 was derived from this alignment.

 

ARFAtOs.phy – a comprehensive alignment of translated A. thaliana sequences with ARF sequences from Oryza sativa.

 

ARFAtOsConsRegions.phy – the same alignment as the previous file, but containing only the conserved regions.  Branching positions of rice ARF sequences indicated in Figure 5 was derived from a neighbor-joining tree constructed from this alignment.

 

IAAPlusARFAtConsRegions.phy – an alignment of translated sequences of conserved regions of the A. thaliana Aux/IAA loci with the motifs III-IV of 7 ARF loci selected to represent the main ARF groups.  Phylogenetic trees constructed from this alignment were used to establish the root positions of the Aux/IAA and ARF trees used in the Remington et al. manuscript.