Supporting tables and figures listed below are provided in the file.
Table A. Distribution and characteristics of SNP sites in five eIF4E genes and neighboring regions in 61 cassava accessions.
Table B. Non-synonymous single nucleotide polymorphisms in five cassava eIF4E genes of 14 cassava accessions.
Table C. Association of SNPs upstream of eIF4E_me gene with CBSD disease responses.
Table D. Information on Illumina RNAseq unpaired reads of two cassava accessions and Bowtie mapping statistics.
Table E. Differential expression analysis of five cassava eIF4E genes in healthy and CBSV infected Albert and Kaleso accessions.
Table F. Information on 454 GS FLX Titanium RNAseq reads of six cassava accessions and Bowtie mapping statistics.
Figure A. Distribution of nucleotide polymorphisms in five cassava eIF4E genes across 10 landraces. High quality Illumina reads of 10 cassava genomes are anchor-aligned to the cassava genome and viewed in IGV. Vertical colored lines indicate nucleotide polymorphisms. Each color represents a different nucleotide substitution. Black dots indicate deletions or missing data. Biallelic variations are clearly visible in certain genes of cassava lines.
Figure B. Alignment of cassava eIF4E proteins with representative plant and human eIF4E proteins. Proteins were aligned with ClustalX 2.0 and manually inspected and adjusted. Shading of similar amino acids and display were performed with BioEdit 7.09. Amino acids conserved in all eIF4E proteins are noted in the consensus line. Eight conserved tryptophan (W) amino acids are indicated with arrows and two involved in cap-binding are indicated in red arrows. Positions of eIF4E proteins where amino acid substitutions resulted in recessive resistance to potyviruses in nature or experimentally are indicated by red six-point stars. Protein sequences of additional eIF4E family proteins were retrieved from NCBI. Protein sources are identified with two letters representing the initials of genus and species, followed by NCBI accession number. At, Arabidopsis thaliana; Ca: Capsicum annuum; Cl, Citrullus lanatus; Cm, Cucumis melo; Cs, Cucumis sativus; Gm, Glycine max; Hs, Homo sapiens; Jc, Jatropha curcas; Ps, Pisum sativum; Pt, Populus trichocarpal; Pv, Phaseolus vulgaris; Rc, Ricinus communis; St, Solanum tuberosum; and Vv, Vitis vinifera.
Figure C. Single nucleotide polymorphisms (SNPs) in the five cassava eIF4E genes and the upstream and downstream 5 kb regions. Data were obtained from combined SNPs and indels from 61 cassava accessions curated at Phytozome (phytozome.jgi.doe.gov). Images of SNPs were rendered in the Genome Browser implemented at the same site. Blue diamonds: synonymous nucleotide substitutions in coding regions or substitutions in non-coding regions; yellow diamonds: non-synonymous substitutions in coding regions; red diamonds: missense substitutions; vertical green lines: indels. Only a 2kb region upstream of nCBP2 is available from the genomic sequence.
Figure D. Expression levels of five eIF4E genes in CBSD-susceptible and -tolerant lines. RNAseq long reads (0.5 kb) specific to each gene from each of the lines generated by the Life Sciences 454 sequencing were counted and normalized to total mapped reads from each sample to generate the FPKM counts. AR37-80, AR40-6, and Mkombozi were susceptible to CBSD while Kiroba, Nachinyaya, and Namikonga were tolerant to CBSD. Raw data were retrieved from NCBI SRA (accessions SRR955444-SRR955447, SRR955449, SRR955450, SRR955453, and SRR955456).