Additional file 2 of Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

Additional file 2: Table S1. Base composition in the plastomes of four Alpinia species. Table S2. List of genes annotated in the plastome of A. galanga. Numbers in parentheses represented the repetition of genes. Superscript T: trans-splicing gene. Table S3. List of genes annotated in the plastome of A. nigra. Numbers in parentheses represented the repetition of genes. Superscript T: trans-splicing gene. Table S4. List of genes annotated in the plastome of A. officinarum. Numbers in parentheses represented the repetition of genes. Superscript T: trans-splicing gene. Table S5. List of genes annotated in the plastome of A. oxyphylla. Numbers in parentheses represented the repetition of genes. Superscript T: trans-splicing gene. Table S6. The length of introns and exons for the splitting genes in the plastome of A. galanga. The gene rps12 was a trans-splicing gene. Table S7. The length of introns and exons for the splitting genes in the plastome of A. nigra. The gene rps12 was a trans-splicing gene. Table S8. The length of introns and exons for the splitting genes in the plastome of A. officinarum. The gene rps12 was a trans-splicing gene. Table S9. The length of introns and exons for the splitting genes in the plastome of A. oxyphylla. The gene rps12 was a trans-splicing gene. Table S10. SSR identified in the plastome of A.galanga. P1 = Mononucleotide; P2 = Di nucleotide; P3 = Tri nucleotide; P4 = Tetra nucleotide; P5 = Penta nucleotide; 6 = Hexa nucleotide repeats and c = Compound repeat microsatellites. Table S11. SSR identified in the plastome of A.nigra. P1 = Mononucleotide; P2 = Di nucleotide; P3 = Tri nucleotide; P4 = Tetra nucleotide; P5 = Penta nucleotide; 6 = Hexa nucleotide repeats and c = Compound repeat microsatellites. Table S12. SSR identified in the plastome of A. officinarum. P1 = Mononucleotide; P2 = Di nucleotide; P3 = Tri nucleotide; P4 = Tetra nucleotide; P5 = Penta nucleotide; 6 = Hexa nucleotide repeats and c = Compound repeat microsatellites. Table S13. SSR identified in the plastome of A. oxyphylla. P1 = Mononucleotide; P2 = Di nucleotide; P3 = Tri nucleotide; P4 = Tetra nucleotide; P5 = Penta nucleotide; 6 = Hexa nucleotide repeats and c = Compound repeat microsatellites. Table S14. Comparison of SSR markers found among four Alpinia species and one outgroup species of Zingiber spectabile. Zisp: Zingiber spectabile; Alga: Alpinia galanga; Alni: Alpinia nigra; Alof: Alpinia officinarum; Alox: Alpinia oxyphylla. Table S15. Dispersed repeat sequences in the plastome of A. galanga. Table S16. Dispersed repeat sequences in the plastome of A.nigra. Table S17. Dispersed repeat sequences in the plastome of A. officinarum. Table S18. Dispersed repeat sequences in the plastome of A. oxyphylla. Table S19. Tandem repeat sequences identified in the plastome of A. galanga. Table S20. Tandem repeat sequences identified in the plastome of A. nigra. Table S21. Tandem repeat sequences identified in the plastome of A.officinarum. Table S22. Tandem repeat sequences identified in the plastome of A.oxyphylla. a: coding sequences; b: intergenic spacers. Table S23. The distances among the shared intergenic spacer (IGS) regions from the five Alpinia plastomes. Alga: Alpinia galanga; Alha: Alpinia hainanensis; Alni: Alpinia nigra; Alof: Alpinia officinarum; Alox: Alpinia oxyphylla. Table S24. The list of accession numbers of the plastome sequences used in the phylogenetic analyses of the Zingiberaceae. Table S25. The dN, dS and dN/dS (ω) value of 77 commom protein-coding genes from plastomes of 21 Alpinia species. Table S26. The two pairs of primers for the ampilification of DNA barcodes. Table S27. The list of sample numbers of the samples used in the species discrimination analyses of the Alpinia.

附加文件2：表S1 4种山姜属（Alpinia）植物质体基因组（plastome）的碱基组成。
表S2 高良姜（A. galanga）质体基因组注释基因列表。括号内数字代表基因拷贝数，上标T表示反式剪接基因（trans-splicing gene）。
表S3 黑山姜（A. nigra）质体基因组注释基因列表。括号内数字代表基因拷贝数，上标T表示反式剪接基因。
表S4 红豆蔻（A. officinarum）质体基因组注释基因列表。括号内数字代表基因拷贝数，上标T表示反式剪接基因。
表S5 益智（A. oxyphylla）质体基因组注释基因列表。括号内数字代表基因拷贝数，上标T表示反式剪接基因。
表S6 高良姜质体基因组中断裂基因的内含子与外显子长度。其中rps12基因为反式剪接基因。
表S7 黑山姜质体基因组中断裂基因的内含子与外显子长度。其中rps12基因为反式剪接基因。
表S8 红豆蔻质体基因组中断裂基因的内含子与外显子长度。其中rps12基因为反式剪接基因。
表S9 益智质体基因组中断裂基因的内含子与外显子长度。其中rps12基因为反式剪接基因。
表S10 高良姜质体基因组中鉴定的简单序列重复（SSR）。其中P1为单核苷酸重复；P2为二核苷酸重复；P3为三核苷酸重复；P4为四核苷酸重复；P5为五核苷酸重复；6为六核苷酸重复，c为复合重复微卫星。
表S11 黑山姜质体基因组中鉴定的简单序列重复（SSR）。其中P1为单核苷酸重复；P2为二核苷酸重复；P3为三核苷酸重复；P4为四核苷酸重复；P5为五核苷酸重复；6为六核苷酸重复，c为复合重复微卫星。
表S12 红豆蔻质体基因组中鉴定的简单序列重复（SSR）。其中P1为单核苷酸重复；P2为二核苷酸重复；P3为三核苷酸重复；P4为四核苷酸重复；P5为五核苷酸重复；6为六核苷酸重复，c为复合重复微卫星。
表S13 益智质体基因组中鉴定的简单序列重复（SSR）。其中P1为单核苷酸重复；P2为二核苷酸重复；P3为三核苷酸重复；P4为四核苷酸重复；P5为五核苷酸重复；6为六核苷酸重复，c为复合重复微卫星。
表S14 4种山姜属植物与1个外类群密苞姜花（Zingiber spectabile）的质体基因组中发现的SSR标记比较。其中Zisp代表密苞姜花；Alga代表高良姜；Alni代表黑山姜；Alof代表红豆蔻；Alox代表益智。
表S15 高良姜质体基因组中的散在重复序列。
表S16 黑山姜质体基因组中的散在重复序列。
表S17 红豆蔻质体基因组中的散在重复序列。
表S18 益智质体基因组中的散在重复序列。
表S19 高良姜质体基因组中鉴定的串联重复序列。
表S20 黑山姜质体基因组中鉴定的串联重复序列。
表S21 红豆蔻质体基因组中鉴定的串联重复序列。
表S22 益智质体基因组中鉴定的串联重复序列。其中a代表编码序列；b代表基因间隔区。
表S23 5种山姜属植物质体基因组共有的基因间隔区（intergenic spacer, IGS）之间的距离。其中Alga代表高良姜；Alha代表海南山姜（Alpinia hainanensis）；Alni代表黑山姜；Alof代表红豆蔻；Alox代表益智。
表S24 姜科（Zingiberaceae）系统发育分析中使用的质体基因组序列登录号列表。
表S25 21种山姜属植物质体基因组中77个共有蛋白编码基因的dN、dS及dN/dS（ω）值。
表S26 用于DNA条形码扩增的2对引物。
表S27 山姜属物种鉴别分析中使用的样品的样品号列表。