Additional file 2 of Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Additional file 2: Table S1. Inversion detect by sniffles in the Nipponbare reference genome. Table S2. The 78 circum-basmati samples with Illumina sequencing result used in this study. Table S3. Names of the Basmati 334 and Dom Sufid genome gene models that had a deletion frequency of zero across the population. Table S4. Names of the Basmati 334 and Dom Sufid genome gene models that had a deletion frequency of above 0.3 and omitted from down stream analysis. Table S5. Orthogroup status for the Basmati 334, Dom Sufid, R498, Nipponbare, and N22 genome gene models. Table S6. Count and repeat types of the presence-absence variation (PAV) in the Basmati 334 or Dom Sufid genome in comparison to the Nipponbare genome. Table S7. Gene ontology results for orthogroups where gene members from the circum-basmati are missing. Table S8. Gene ontology results for orthogroups where gene members from circum-aus, indica, and japonica are missing. Table S9. Population frequency across the 78 circum-basmati samples for orthogroups that were specifically missing a gene in the Basmati 334 and Dom Sufid genome gene models. Table S10. Genome coordinates of the LTR retrotransposons of the Basmati 334 genomes. Table S11. Genome coordinates of the LTR retrotransposons of the Dom Sufid genomes. Table S12. Genome coordinates of the Gypsy elements indicated with a single star in Fig. 3. Table S13. Genome coordinates of the Copia elements indicated with a single star in Fig. 3. Table S14. Genome coordinates of the Gypsy elements indicated with a double star in Fig. 3. Table S15. Genome coordinates of the Copia elements indicated with a triple star in Fig. 3. Table S16. The 82 Oryza population samples with Illumina sequencing result used in this study. Table S17. a i parameter estimates for the 13 different demographic models. See Additional file 1: Figure S9 for visualization of the estimating parameters.

附加文件2：表S1。经Sniffles检测得到的日本晴（Nipponbare）参考基因组倒位变异。
表S2。本研究中使用的78份具有Illumina测序数据的泛巴斯马蒂（circum-basmati）样本。
表S3。群体中缺失频率为0的巴斯马蒂334（Basmati 334）与Dom Sufid基因组基因模型名称。
表S4。群体中缺失频率高于0.3且被排除于下游分析之外的巴斯马蒂334与Dom Sufid基因组基因模型名称。
表S5。巴斯马蒂334、Dom Sufid、R498、日本晴（Nipponbare）与N22基因组基因模型的直系同源基因簇（orthogroup）归属状态。
表S6。相较于日本晴参考基因组，巴斯马蒂334与Dom Sufid基因组中存在-缺失变异（presence-absence variation, PAV）的数量及重复序列类型。
表S7。泛巴斯马蒂类群缺失基因成员的直系同源基因簇的基因本体（Gene Ontology）富集分析结果。
表S8。泛Aus（circum-aus）、籼稻（indica）与粳稻（japonica）类群缺失基因成员的直系同源基因簇的基因本体富集分析结果。
表S9。仅在巴斯马蒂334与Dom Sufid基因组基因模型中缺失基因的直系同源基因簇在78份泛巴斯马蒂样本中的群体分布频率。
表S10。巴斯马蒂334基因组中的长末端重复序列反转录转座子（long terminal repeat retrotransposon, LTR retrotransposon）基因组坐标信息。
表S11。Dom Sufid基因组中的长末端重复序列反转录转座子基因组坐标信息。
表S12。图3中单星号标注的Gypsy反转录转座子元件基因组坐标信息。
表S13。图3中单星号标注的Copia反转录转座子元件基因组坐标信息。
表S14。图3中双星号标注的Gypsy反转录转座子元件基因组坐标信息。
表S15。图3中三星号标注的Copia反转录转座子元件基因组坐标信息。
表S16。本研究中使用的82份具有Illumina测序数据的稻属（Oryza）群体样本。
表S17。13种不同群体遗传学模型的a_i参数估计值。估算参数的可视化结果详见附加文件1：图S9。