Fig 1.
(A) Consensus distribution of motifs in all Viridiplantae sequences. (B) Distribution of motifs across 67 representative Viridiplantae CLO/PXG proteins grouped in eight taxonomic clades as follows. (i) Trebouxiophyceae, (ii) Chlorophyceae, (iii) Charophyta, (iv) Non-seed plants, (v) Gymnosperms, (vi) basal Angiosperms, (vii) Monocots and (viii) Dicots.(C) Sequences of the 7 major motifs found in Viridiplantae CLO/PXG proteins.
Fig 2.
Sequence alignments of CLO/PXG protein families from three representative Charophyte species plus 67 sequences from 34 species across the Viridiplantae.
(A) Klebsormidium nitens alignment. (B) Oryza sativa alignment. (C) Arabidopsis thaliana alignment. (D) 67 protein sequences alignment from 34 Viridiplantae species. The five major structural domains are shown respectively as the N-terminal H-caleosin, Ca 2+ binding EF Hand, Lipid-binding, Heme binding and kinase phosphorylation and C-terminal kinase phosphorylation domains. The proline knot region and two conserved Histidines are also shown.
Fig 3.
Phylogenetic analysis of 67 CLO/PXG sequences.
(A) 67 CLO/PXG sequences from 34 species across the Viridiplantae. (B) 67 CLO/PXG sequences from 34 species across the Viridiplantae plus six selected fungal species.
Fig 4.
Transcriptome analysis of CLO/PXG gene expression in date palm and oil palm tissues.
(A) The oil palm genome P5-build was used to read map the RNA seq data from Roche 454 reads (a full dataset is available from NCBI BioProject PRJNA201497). Reads from Roche/454-derived libraries were assembled into isotigs, which were blasted onto Arabidopsis thaliana gene models with a threshold of E-value < 10−5. The best-hit A. thaliana gene model was assigned to the homologue of the query isotig. To estimate expression levels of genes in mesocarp and kernel tissues, Illumina HiSeq 2000 reads from each library were mapped to assembled isotigs from all Elaeis guineensis reads by using the Burrows–Wheeler Aligner. Gene group expression levels were calculated as the number of mapped reads on each isotig divided by the total number of isotigs, multiplied by 100,000, and scaled by the number of genes in each gene group. Both copy number and read coverage were the mean of measures from two biological replicates. Data were analysed as described above for Roche/454 data, except that expression levels were calculated as transcripts per million tags. Identification of expression caleosin in oil palm was done using open source Tuxedo suite software[50]. (B) Transcriptional analysis of CLO/PXG gene expression in date palm tissues and treatments as follows: a) exposure to 0, 10 and 100 ng.L-1 of the dioxin, TCDD; b) drought for 2, 4 and 6 days; c) exposure to 0, 150 and 300 ng.L-1 NaCl. Seedlings with a radicle length of 0.5 or 2 or 4.5 cm were referred as stage I, II and III respectively.
Fig 5.
Presence of CLO/PXG sequences across the Viridiplantae and their estimated evolutionary divergence times.
The major taxa that contain CLO/PXG sequences are shown as blue-shaded boxes. Individual species with one or more CLO/PXG sequences are shown in blue while other species where CLO/PXG sequences are definitely absent from their genomes are shown in brown. The estimated evolutionary divergence times of selected key taxa are shown as the number of million years ago (My). Starred major taxa are those with good evidence of monophyletic status while non-starred taxa are probably polyphyletic or paraphyletic.
Fig 6.
Alignments of anomalous CLO/PXG sequences from two non-Viridiplantae species.
(A) Alignments of seven CLO/PXG sequences from S. cellulosum. (B) Alignments of two CLO/PXG sequences from C. owczarzaki with a range of green algal sequences. (C) Alignments of five putative CLO/PXG sequences from the Metazoan nematode genus, Panagrolaimus spp, with sequences from A. thaliana.