Additional file 2: Table S1. of PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

The list of restriction enzymes being used by PhytoCRISP-Ex. (XLSX 13 kb

Additional file 1: Figure S1. of PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

PhytoCRISP-Ex efficacy. The scatter plot depicts that most of the predicted Cas9 targets per gene in Thalassiosira pseudonana and Phaeodactylum tricornutum, respectively, are potential candidates (passing both PhytoCRISP-Ex filter). X-axis represents the percent efficiency of each gene in terms of having high number of potential Cas9 targets compared to the total number of targets. Y-axis represents the number of all potential targets per gene. (PDF 182 kb

Additional file 4: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S3. Comparison of GC content at the third codon position (dGC3) between pairs of homoeologous genes in each homoeologous chromosome. The vertical axis represents the dGC3 value of each homoeologous gene, and horizontal axis indicates the relative number of homoeologous genes on each chromosome. The dGC3 value indicates the ratio of GC content at the third codon position in each homoeologous gene with respect to its corresponding pair, so if the dGC3 value is over 1 (above the horizontal axis), its GC content is higher than the other pair. Red and green lines correspond to the global GC content of chromosome; red lines indicate the dGC3 value of homoeologous gene along the homoeologous chromosome with higher global GC content and green lines indicate the dGC3 value of the gene along the homoeologous chromosome with lower global GC content. The profile of dGC3 showed perfect consistency with dGC (Fig. 1) and approximately twice more difference than dGC. We also calculated the GC content ratio of first and second codon positions; however consistency to dGC was low. This suggests that the differences in dGC of the two subgenomes was mainly derived from the GC content ratio of the third codon position. (PDF 137 kb

Additional file 1: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S1. Structure of dGC flip over region on chromosome 10. (A) Orange and blue colors of the pentagon arrows represent the different dGC values in corresponding homoeologous genes; orange indicates the genes with relatively higher dGC and blue indicates the genes with relatively lower dGC within the pair. Each homoeologous gene pair are connected with dotted lines. The horizontal dotted line at the ends of some of the scaffolds indicates that the scaffold continues beyond what is shown in the figures. The gene map is not drawn to scale. (B) Scaffold assembly of dGC flip over region in chromosome 10′, which is rounded by red line in (A), was validated by PCR. The schematic figure represents the 8 amplified regions in PCR experiment. Vertically printed numbers indicate the base position within the scaffold. Each amplified region has overlapped region to the next. Primers for this experiment was designed to annealed on either non-coding region or non-homoeologous gene region, to avoid the non-specific amplification of paired homoeologous gene. (C) Length of PCR products were analyzed by electrophoresis through a 0.8% (wt/vol) agarose gel. Indicated lane numbers are corresponding to the amplified region shown in (B). (PDF 69 kb

Additional file 3: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S2. Codon usage frequency of subgenomes Fso_h and Fso_l. (A) Codon usage frequency of each of the subgenomes are compared with genomes of the model diatoms P. tricornutum and T. pseudonana. Codon usage of P. tricornutum and T. pseudonana were calculated from the nucleotide FASTA file of the newest version of filtered gene models (v2.0 for P. tricornutum (Phatr2) and v3.0 for T. pseudonana (Thaps3)) downloaded from the genome portal of the Department of Energy Joint Genome Institute (JGI) [80]. (B) Codon usage frequency of the subgenomes ordered in coding amino acids and (C) ratio of usage between Fso_h and Fso_l. Dots show the ratio of codon usage (right y-axis). Red line indicates the equal ratio, therefore the codons with the usage ratio above the red line are more frequently used in Fso_h subgenome, whereas codons with the usage ratio beneath the red line are more frequently used in Fso_l subgenome. (PDF 110 kb

Additional file 5: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S4. PCA based on codon usage frequency of dGC flip over region on chromosome 10. PCA based on codon usage frequency of dGC flip over region on chromosome 10. 10_Fso_h and _l represents the PCA result of all homoeologous genes on chromosome 10 with our tentative classification described in the Results section. These values are identical to “10” represented in Fig. 2. 10_A and 10_B represents the PCA results of chromosome 10 (high global GC content), _A includes the homoeologous genes located in the upstream region of dGC flip and _B includes the homoeologous genes located downstream. 10′_A and 10’_B represents the PCA result of corresponding region in chromosome 10′ (low global GC content). (PDF 37 kb

Additional file 9: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S8. Range of homoeolog expression bias in metabolic pathways. Box plot of log2 showing the expression ratio of homoeologous gene pairs in each metabolic pathway. Red dotted line indicates the equal ratio log2. Black dotted line indicates the threshold of expression ratio where the homoeologous gene pair is defined as biased (log2FC > 1). The orange and blue colors of the box indicate the direction of homoeolog expression bias, towards Fso_h and Fso_l, respectively. (PDF 37 kb

Additional file 11: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S10. Comparison of GC content ratio between orthologous pair of Thalassiosira oceanica and T. pseudonana. 6463 orthologs of T. oceanica and T. pseudonana were discovered by sequence homology analysis and GC content ratio (dGC) were calculated. Vertical axis represents dGC value of each orthologs. The dGC values of orthologs along the T. oceanica and T. pseudonana were indicated as red and green line, respectively. The dGC plots for individual chromosomes were not prepared because the genome sequence of T. oceanica was not assembled into each chromosome. (PDF 151 kb

Additional file 7: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Figure S6. GO terms of consistently biased homoeologous genes. Figure shows the frequency of GO terms, annotated to the second depth, within the group of homoeologous genes which were consistently biased towards Fso_h or Fso_l (corresponding to the genes in the histogram of Fig. 3b). Orange and blue colors represent the direction of homoeolog expression bias of the group, Fso_h and Fso_l, respectively. Dots in the figure represent the log ratio of frequency of corresponding GO terms between Fso_h-biased group and Fso_l-biased group. (PDF 279 kb