Additional file 2: of Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

Table S1. Codon usage in genome and subgenome of F. solaris. Codon usage in (A) genome and (B) subgenome of F. solaris in per mil. (A) The table includes the codon usage of all genes predicted in F. solaris, including homoeologous genes, non-homoeologous genes, and genes predicted on scaffolds not assembled on chromosomes. (B) The table includes the codon usage of homoeologous genes and non-homoeologous genes in each subgenome. The values corresponding to Fso_h and Fso_l were written in left (bold) and right (italic) of each column, respectively. Values in parentheses represent the ratio of codon usage between Fso_h and Fso_l (Fso_h / Fso_l); Table S2. Top 10 and bottom 10 loadings of PC1 and PC2 from the PCA based on codon usage frequency; Table S3. tRNA genes discovered in each subgenome of F. solaris; Table S4. Nucleotides sequence motifs discovered in promoter region of consistently biased homoeologous genes in F. solaris; Table S5. Lists of genes which contained the motif TABASTA in promoter region. (XLSX 183 kb)

附表S1：太阳杆菌（F. solaris）基因组与亚基因组的密码子使用（codon usage）情况。本附表以千分比形式呈现（A）太阳杆菌基因组及（B）其亚基因组的密码子使用偏性。其中，（A）板块收录了太阳杆菌所有预测基因的密码子使用数据，包括同源异型基因（homoeologous genes）、非同源异型基因（non-homoeologous genes），以及锚定在未组装至染色体的支架（scaffold）上的预测基因。（B）板块则涵盖各亚基因组中同源异型基因与非同源异型基因的密码子使用数据。每一列中，Fso_h与Fso_l对应的数值分别以左侧加粗字体、右侧斜体字体标注；括号内的数值为Fso_h与Fso_l的密码子使用比值（Fso_h / Fso_l）。
附表S2：基于密码子使用频率的主成分分析（PCA, Principal Component Analysis）中，PC1与PC2的前10位、后10位载荷值。
附表S3：太阳杆菌各亚基因组中鉴定得到的转运RNA（tRNA, transfer RNA）基因。
附表S4：太阳杆菌中表达偏性一致的同源异型基因的启动子区域内发现的核苷酸序列基序（sequence motif）。
附表S5：启动子区域含有TABASTA序列基序的基因列表。（XLSX 183 kb）