Supporting material | Chan et al. 2011 Current Biology 21(4): 328-333 | doi:10.1016/j.cub.2011.01.037

Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes

Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM and Bhattacharya (2011) Current Biology, 21(4): 328-333. | doi | pubmed

DATA: Porphyridium cruentum CCMP1328
Assembled ESTs (unigenes) of P. cruetum (36,167) in FASTA Download (.fasta, 23MB)
Proteins of P. cruentum 6-frame translated from the assembled ESTs (6 x 36,167 = 217,002) in FASTA Download (.faa, 55MB)
P. cruentum proteins with significant hits [e-value <= 1e-10] (13,632) in FASTA Download (.zip, 144MB)
Protein sequence alignments (13,632) in FASTA Download (.zip, 12MB)
Protein sequence alignments, after GBLOCKS refinement (12,003) in PHYLIP
(these are used to build the phylogenies)
Download (.zip, 66MB)
RAxML phylogenetic trees (12,003) in NEWICK Download (.zip, 29MB)
Annotations of P. cruentum proteins in TXT Download (.txt, 3.1MB)
All 386,903 EST reads generated from this work are available at NCBI dbEST, accession numbers HS588189-HS975091.

DATA: Calliarthron tuberculosum partial genome
Protein models of C. tuberculosum based on AUGUSTUS prediction (23,961) in FASTA Download (.faa, 5.6MB)
The partial genome data (454 reads) are available from NCBI Short Read Archive accession SRP005182.

RESULTS: Sorted RAxML trees
Trees supporting monophyly of red algae with other phyla (ref. Figure 1D)
Number of terminal taxa per tree (N) >= 4, boostrap >= 90% (1,367 with eukaryotes, 318 with prokaryotes)
Download (.zip, 1.7MB)
Trees supporting monophyly of red algae with other phyla (ref. Figure S1)
Number of terminal taxa per tree (N) >= 4, boostrap >= 70% (2,167 with eukaryotes, 431 with prokaryotes)
Download (.zip, 3.3MB)
Trees supporting gene sharing history between red+green algal lineages with other phyla (1,808; see main text)
Number of phyla per tree >= 3, number of terminal taxa per tree (N) >= 30, boostrap >= 90
Download (.zip, 5.7MB)
Trees supporting gene sharing history between red+green algal lineages with other phyla (2,017)
Number of phyla per tree >= 3, number of terminal taxa per tree (N) >= 30, boostrap >= 70%
Download (.zip, 6.5MB)

©2010-2011 Cheong Xin Chan and Debashish Bhattacharya at Rutgers, The State University of New Jersey. Updated February 21, 2011