Supplemental material for "The cellulose synthase superfamily in fully sequenced plants and algae"



  1. Fasta format full length sequences of each Csl proteins (description line: >ID|originalID_from_Genome_Release)
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families)

  2. Csl gene ID and family name mapping file (which Csl gene belongs to which Csl family)

  3. Fasta format Pfam domain sequences of each Csl proteins (description line: >ID|domain|Evalue)
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families)

  4. Original multiple sequence alignment of full length proteins using MAFFT L-INS-i method
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families) and phylogeny

  5. Modified multiple sequence alignment of full length proteins using MAFFT L-INS-i method
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families) and phylogeny

  6. Original multiple sequence alignment of full length proteins using MAFFT E-INS-i method
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families) and phylogeny

  7. Modified multiple sequence alignment of full length proteins using MAFFT E-INS-i method
    1. download Csl proteins with Pfam Glycos_transf_2 domain (CslA and CslC families)
    2. download Csl proteins with Pfam Cellulose_synt domain (other Csl families) and phylogeny

  8. Comparative study of individual families: CesA, CslD, CslF, CslA and CslC (download)

  9. MEGA4 NJ trees (download)
    Legend:A) 217 plant proteins (see Legend of Figure 1) and two cyanobacterial proteins (see Legend of Figure 6) that have the Pfam Cellulose_synt domain were used to construct this tree. B) 88 proteins (see Legend of Figure 1) that have the Pfam Glycos_transf_2 domain were used to construct the tree. Both the full length proteins and the conserved Pfam domain regions were used in the phylogeny reconstruction and the corresponding bootstrap values were shown respectively.

  10. PhyML tree for 88 CslA/C proteins and 11 other GT2 proteins (download)
    Legend:88 CslA/C proteins (See legend of Figure 1) and 11 other GT2 proteins were used to construct the tree. The 11 proteins include one protein from Physcomitrella patens, seven proteins from Selaginella moellendorffii, one protein from the red alga Cyanidioschyzon merolae and three proteins from the two Ostreococcus green algae have the Pfam GT2 domain and are homologous to land plant CslA/C proteins.

  11. PhyML tree for CslA/C homologs in Refseq DB (download)
    Legend:The ML phylogeny of the CslA/C families and their close homologs in the Refseq DB. Sequences in the down diagram were taken from the light blue coded area of the up diagram. The groups with the green background are plant and algal proteins, and the groups with the light blue background are proteins from other life kingdoms, mostly from prokaryotes. The down tree shows that the prokaryotic GT2 group A possibly has contributed to the origin of CslA/C genes in eukaryotes, either with the Mitochondria endosymbiosis or other very ancient lateral gene transfer. But they are unlikely to be transferred from Cyanobacteria, as what had been reported for the plant CesA and other Csl families.