Additional file 14 of Genomic insights into positive selection during barley domestication

Additionalfile 14: Table S1. Statistics of orthologs, syntenic gene pairs, and syntenic blocks. Table S2. The Ka, Ks, and Ka/Ks values for 9,176 and 6,483 single-copy orthologous genes between wild barley and landrace, and between landrace, and improved cultivar, respectively. Table S3. Correlation analysis of substitution rate, gene feature, and codon usage bias.(The Ka, Ks, and Ka/Ks values were calculated between wild barley and landrace). Table S4. Correlation analysis of substitution rate, gene feature, codon usage bias and expression pattern. (The Ka, Ks, and Ka/Ks values were calculated between landrace and improved barley). Table S5. Distributions of Ka/Ks values between wild barley and landrace, and between landrace and improved cultivar. Table S6. Comparisons of evolutionary rate, gene property, codon usage bias between PSGs and NSGs in barley. Table S7. Comparisons of expression patterns between PSGs and NSGs in barley. Table S8. Statistics of codon usage bias indicators. Table S9. Distributions of transcription factor gene family for different orthologous groups. Table S10. Statistics of the 49 representative transcription factor gene families. Table S11. The detail information of positively selected transcription factors. Table S12. GO enrichment analysis of PSGs. Table S13. KEGG pathway enrichment analysis of PSGs. Table S14. Distributions of PSG-related and NSG-related SNPs. Table S15. Tracy-Widom test for the first five eigenvectors in the PCA. Table S16. Nucleotide diversity (π) analysis between PSGs and NSGs. Table S17.Comparisons of FST values between PSGs and NSGs within different genomic regions. Table S18. SNPs distributions, nucleotide diversities, haplotypes, and expression patterns of candidate genes. Table S19. Accession numbers and sample information of the RNA-seq data used in this study. Table S20. Accession numbers and information of the 85 wild barley and 133 landrace accessions.补充文件14： 表S1 直系同源基因、共线性基因对及共线性区块的统计分析 表S2 分别针对野生大麦与地方品种间的9176个单拷贝直系同源基因，以及地方品种与改良栽培品种间的6483个单拷贝直系同源基因，统计其Ka、Ks及Ka/Ks值 表S3 替换速率、基因特征与密码子使用偏好性的相关性分析（该分析基于野生大麦与地方品种间计算得到的Ka、Ks及Ka/Ks值） 表S4 替换速率、基因特征、密码子使用偏好性与表达模式的相关性分析（该分析基于地方品种与改良栽培大麦间计算得到的Ka、Ks及Ka/Ks值） 表S5 野生大麦与地方品种、地方品种与改良栽培品种间的Ka/Ks值分布情况 表S6 大麦中正选择基因（positively selected gene, PSG）与非正选择基因（non-positively selected gene, NSG）间的进化速率、基因属性及密码子使用偏好性比较 表S7 大麦中正选择基因与非正选择基因间的表达模式比较 表S8 密码子使用偏好性指标的统计分析 表S9 不同直系同源类群的转录因子基因家族分布情况 表S10 49个代表性转录因子基因家族的统计分析 表S11 正选择转录因子的详细信息 表S12 正选择基因的基因本体论（Gene Ontology, GO）富集分析 表S13 正选择基因的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析 表S14 正选择基因及非正选择基因相关单核苷酸多态性（single nucleotide polymorphism, SNP）的分布情况 表S15 主成分分析（Principal Component Analysis, PCA）中前5个特征向量的Tracy-Widom检验 表S16 正选择基因与非正选择基因间的核苷酸多样性（π）分析 表S17 不同基因组区域内，正选择基因与非正选择基因间的FST值比较 表S18 候选基因的单核苷酸多态性分布、核苷酸多样性、单倍型及表达模式 表S19 本研究所用RNA测序（RNA-seq）数据的登录号与样本信息 表S20 85份野生大麦与133份地方品种大麦种质的登录号及相关信息