MOESM1 of Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype
Creators: name: Traller, Jesse
name: Cokus, Shawn
name: Lopez, David
name: Gaidarenko, Olga
name: Smith, Sarah
name: McCrow, John
name: Gallaher, Sean
name: Podell, Sheila
name: Thompson, Michael
name: Cook, Orna
name: Morselli, Marco
name: Jaroszewicz, Artur
name: Allen, Eric
name: Allen, Andrew
name: Sabeeha Merchant
name: Pellegrini, Matteo
name: Hildebrand, Mark
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 1. Additional methods and figures. Figure S1. (a) Cyclotella cryptica nuclear assembly overview broken down by minimum contig size (Kbp) versus total Mbp of all contigs (left) and minimum contig size versus the total number of contigs (right) and (b) genomic sequencing data. Table S1. Statistics from different gene model prediction pipelines. The pipelines are: (1) FGENESH gene predictions, Diatom training set, (2) Augustus gene predictions V1, Chlamydomonas training set, no RNAseq data, (3) Augustus gene predictions V2, FGENESH100 training set, RNAseq data (4) Augustus gene predictions V3, ‘self’ trained, RNAseq data (5) MAKER gene predictions, (Augustus self trained + FGENESH + GeneMarkES). Details are presented in Additional methods. Data presented includes all predicted models regardless of read counts from RNAseq data and prior to removing apparent duplicate contigs (Additional methods, Genome Library Construction and Sequencing). Table S2. Repeat sequences in C. cryptica identified using (a) RepBase data and (b) RepeatModeler data. Figure S2. Phylogenetic comparison of diatom species with sequenced genomes. (a) 18S sequence comparison from [91], accession numbers are listed in Additional file 4. (b) Reciprocal best blast hits comparison. C. cryptica and T. pseudonana are the most similarly related centric diatoms with available genomic data. Figure S3. Per-cytosine fraction methylation. (a) 0 h, silicon replete sample (b) 48 h, silicon-deplete sample. All sites shown have a read coverage greater than or equal to 4. Figure S4. Per-site methylation differences between silicon replete and deplete conditions. (a) Histogram showing absolute value of the difference between 48 and 0 h. (b) Scatter plot showing the slope between fraction methylation of genes when comparing the two conditions is linear, outliers are apparent. Figure S5. Fraction methylation across the eight largest contigs in C. cryptica. Blue is 0 h silicon replete sample, red is 48 h silicon-deplete sample. AUGUSTUS V3 models (labeled “Gene”) are depicted in black while repeat modeler data are depicted in gray. X-axis is number of kilobase pairs in the contig. Figure S6. Binned repeats (a) and fraction methylation across gene body (b) in C. cryptica. Table S3. Summary of gene methylation (AUGUSTUS V3 models) in both experimental conditions. Figure S7. Gene methylation relative to gene expression. (a) Three populations emerged (red boxes i–iii) when comparing average fraction methylation to Log2 FPKM. (b) Gene count binned according to FPKM and shaded according to methylation status. Line depicts the proportion of methylated genes per bin. Data shown is for silicon replete, 0 h condition. Figure S8. Vector map for ribosomal protein L41 construct for C. cryptica.