园艺学报 ›› 2022, Vol. 49 ›› Issue (2): 407-415.doi: 10.16420/j.issn.0513-353x.2021-0058
收稿日期:
2021-05-20
修回日期:
2021-12-17
出版日期:
2022-02-25
发布日期:
2022-02-28
通讯作者:
邓崇岭
E-mail:cldeng88168@126.com
基金资助:
WU Xiaoxiao, CHEN Chuanwu, LIU Ping, TANG Yan, DENG Chongling()
Received:
2021-05-20
Revised:
2021-12-17
Online:
2022-02-25
Published:
2022-02-28
Contact:
DENG Chongling
E-mail:cldeng88168@126.com
摘要:
对4个广西姑婆山野生柑橘、1个枳、1个金柑以及14个其他柑橘进行全基因组重测序,每个样本测序数据量约为16 Gb,平均测序深度为54×。通过基因组比对、SNP检测、PCA主成分分析、邻接法构建系统发育进化树,分析广西贺州姑婆山野生柑橘资源遗传多样性、群体结构及分类地位。从20份样品中,共检测出6 782 158个高质量SNP位点。基于这些SNP位点,根据PCA主成分分析和系统进化树分析结果,可将20份样本分为3类:广西姑婆山野柑与莽山野柑聚为一类,金柑与其他柑橘聚为一类,枳聚为单独一类。该研究表明姑婆山野生柑橘资源与莽山野柑一样具有原始性和独特性,应该为独立的属或者柑橘属中独立的种。
中图分类号:
武晓晓, 陈传武, 刘萍, 唐艳, 邓崇岭. 基于重测序的广西姑婆山野生柑橘资源遗传演化及分类地位分析[J]. 园艺学报, 2022, 49(2): 407-415.
WU Xiaoxiao, CHEN Chuanwu, LIU Ping, TANG Yan, DENG Chongling. Genetic Evolution and Taxonomic Status Analysis of Wild Citrus Resources Based on Resequencing in Guposhan Mountain in Guangxi Province[J]. Acta Horticulturae Sinica, 2022, 49(2): 407-415.
名称 Name | 叶身 leaf shape | 叶尖 Leaf tip | 叶基 Leaf base | 叶缘 Leaf margin | 叶柄长/cm Petiole length | 叶片长/cm Leaf length | 叶片宽/cm Leaf width | 叶形指数 Leaf type index |
---|---|---|---|---|---|---|---|---|
皱皮柑2号 Zhoupigan 2 | 圆形 Round | 钝圆 Blunt round | 广楔形 Wide wedge | 锯齿缘 Serrated edge | 0.87 ± 0.21 | 4.24 ± 0.85 | 2.32 ± 0.32 | 1.83 ± 0.27 |
皱皮柑5号 Zhoupigan 5 | 菱形 Diamond | 钝圆 Blunt round | 楔形 Wedge | 全缘 All edge | 0.96 ± 0.16 | 4.25 ± 0.92 | 2.29 ± 0.24 | 1.86 ± 0.43 |
皱皮柑6号 Zhoupigan 6 | 菱形 Diamond | 钝圆 Blunt round | 楔形 Wedge | 全缘 All edge | 1.00 ± 0.25 | 5.41 ± 0.93 | 2.77 ± 0.58 | 1.95 ± 0.20 |
姑婆山野生元橘 Sinocitrus chuana | 菱形 Diamond | 短尖 short-pointed | 狭楔形 Narrow wedge | 浅波缘 Shallow edge | 0.92 ± 0.13 | 4.85 ± 0.56 | 2.32 ± 0.19 | 2.09 ± 0.33 |
表1 广西姑婆山4个野生柑橘资源叶片形状差异
Table 1 Differences in leaf of four wild citrus resources in Guposhan Mountain in Guangxi Province
名称 Name | 叶身 leaf shape | 叶尖 Leaf tip | 叶基 Leaf base | 叶缘 Leaf margin | 叶柄长/cm Petiole length | 叶片长/cm Leaf length | 叶片宽/cm Leaf width | 叶形指数 Leaf type index |
---|---|---|---|---|---|---|---|---|
皱皮柑2号 Zhoupigan 2 | 圆形 Round | 钝圆 Blunt round | 广楔形 Wide wedge | 锯齿缘 Serrated edge | 0.87 ± 0.21 | 4.24 ± 0.85 | 2.32 ± 0.32 | 1.83 ± 0.27 |
皱皮柑5号 Zhoupigan 5 | 菱形 Diamond | 钝圆 Blunt round | 楔形 Wedge | 全缘 All edge | 0.96 ± 0.16 | 4.25 ± 0.92 | 2.29 ± 0.24 | 1.86 ± 0.43 |
皱皮柑6号 Zhoupigan 6 | 菱形 Diamond | 钝圆 Blunt round | 楔形 Wedge | 全缘 All edge | 1.00 ± 0.25 | 5.41 ± 0.93 | 2.77 ± 0.58 | 1.95 ± 0.20 |
姑婆山野生元橘 Sinocitrus chuana | 菱形 Diamond | 短尖 short-pointed | 狭楔形 Narrow wedge | 浅波缘 Shallow edge | 0.92 ± 0.13 | 4.85 ± 0.56 | 2.32 ± 0.19 | 2.09 ± 0.33 |
名称 Name | 着生 Implantation position | 花粉量 Pollen quantity | 花丝 Filament state | 花瓣数 Number of petals | 花瓣长/cm Petals length | 花瓣宽/cm Petal width | 雄蕊数/个 Number of stamens | 花丝长/cm Filaments length | 花柱长/cm Style length |
---|---|---|---|---|---|---|---|---|---|
皱皮柑2号 Zhoupigan 2 | 丛生 Cluster state | 中等 Moderate | 分离 Separate | 4.95 ± 0.22 | 1.28 ± 0.10 | 0.68 ± 0.05 | 22.88 ± 1.32 | 0.75 ± 0.07 | 0.14 ± 0.09 |
皱皮柑5号 Zhoupigan 5 | 丛生 Cluster state | 多 Abundant | 分离 Separate | 4.95 ± 0.37 | 1.18 ± 0.08 | 0.67 ± 0.08 | 22.10 ± 1.65 | 0.66 ± 0.07 | 0.11 ± 0.04 |
皱皮柑6号 Zhoupigan 6 | 丛生 Cluster state | 中等 Moderate | 分离 Separate | 4.67 ± 0.47 | 1.72 ± 0.14 | 0.68 ± 0.07 | 24.10 ± 2.12 | 1.09 ± 0.09 | 0.83 ± 0.31 |
姑婆山野生元橘 Sinocitrus chuana | 单生 Solitary state | 中等 Moderate | 部分联合 Partial union | 4.53 ± 0.40 | 0.94 ± 0.14 | 0.48 ± 0.04 | 23.12 ± 0.63 | 0.56 ± 0.18 | 0.14 ± 0.09 |
表2 广西姑婆山4个野生柑橘资源花性状差异
Table 2 Differences in flower of four wild citrus resources in Guposhan Mountain in Guangxi Province
名称 Name | 着生 Implantation position | 花粉量 Pollen quantity | 花丝 Filament state | 花瓣数 Number of petals | 花瓣长/cm Petals length | 花瓣宽/cm Petal width | 雄蕊数/个 Number of stamens | 花丝长/cm Filaments length | 花柱长/cm Style length |
---|---|---|---|---|---|---|---|---|---|
皱皮柑2号 Zhoupigan 2 | 丛生 Cluster state | 中等 Moderate | 分离 Separate | 4.95 ± 0.22 | 1.28 ± 0.10 | 0.68 ± 0.05 | 22.88 ± 1.32 | 0.75 ± 0.07 | 0.14 ± 0.09 |
皱皮柑5号 Zhoupigan 5 | 丛生 Cluster state | 多 Abundant | 分离 Separate | 4.95 ± 0.37 | 1.18 ± 0.08 | 0.67 ± 0.08 | 22.10 ± 1.65 | 0.66 ± 0.07 | 0.11 ± 0.04 |
皱皮柑6号 Zhoupigan 6 | 丛生 Cluster state | 中等 Moderate | 分离 Separate | 4.67 ± 0.47 | 1.72 ± 0.14 | 0.68 ± 0.07 | 24.10 ± 2.12 | 1.09 ± 0.09 | 0.83 ± 0.31 |
姑婆山野生元橘 Sinocitrus chuana | 单生 Solitary state | 中等 Moderate | 部分联合 Partial union | 4.53 ± 0.40 | 0.94 ± 0.14 | 0.48 ± 0.04 | 23.12 ± 0.63 | 0.56 ± 0.18 | 0.14 ± 0.09 |
样品 编号 Sample | 资源 Resource | 总Reads数 Total reads | 总碱基数/bp Total base | 比对Reads数 Comparison reads | 总比对率/% Total ratio | 双端比对率/% Double-terminal ratio | 平均测序深度(×) Average sequencing depth |
---|---|---|---|---|---|---|---|
S01 | 枳Poncirus trifoliata | 107 697 496 | 16 154 624 400 | 99 286 290 | 92.19 | 76.67 | 53.60 |
S02 | 阳朔金柑Fortunella ‘Yangshuo Jingan’ | 89 529 554 | 13 429 433 100 | 83 875 162 | 93.68 | 79.89 | 44.56 |
S03 | 红河大翼橙 Citrus hongheensis | 98 195 835 | 14 729 375 250 | 90 439 245 | 92.10 | 78.80 | 48.88 |
S04 | 龙胜小江村宜昌橙 C. ichangensis ‘Longsheng Xiaojiangcun’ | 109 088 887 | 16 363 333 050 | 103 907 427 | 95.25 | 81.29 | 54.30 |
S05 | 莽山野柑(尖叶) C. mangshanensis (pointed leaf) | 107 753 893 | 16 163 083 950 | 103 036 387 | 95.62 | 81.53 | 53.63 |
S06 | 莽山野柑(圆叶) C. mangshanensis (round leaf) | 103 687 777 | 15 553 166 550 | 99 627 681 | 96.08 | 82.54 | 51.61 |
S07 | 姑婆山野生皱皮柑2号 Guposhan Wild Zhoupigan 2 | 103 255 191 | 15 488 278 650 | 98 252 313 | 95.15 | 81.28 | 51.39 |
S08 | 姑婆山野生皱皮柑5号 Guposhan Wild Zhoupigan 5 | 118 238 006 | 17 735 700 900 | 110 819 337 | 93.73 | 79.74 | 58.85 |
S09 | 姑婆山野生皱皮柑6号 Guposhan Wild Zhoupigan 6 | 92 758 407 | 13 913 761 050 | 85 643 147 | 92.33 | 78.24 | 46.17 |
S10 | 姑婆山野生元橘 Sinocitrus chuana Tseng | 112 921 407 | 16 938 211 050 | 107 256 623 | 94.98 | 81.75 | 56.21 |
S11 | 道县野橘C. daoxianensis | 107 933 335 | 16 190 000 250 | 104 004 963 | 96.36 | 88.68 | 53.72 |
S12 | 立花橘C. tachibana | 109 720 035 | 16 458 005 250 | 105 353 025 | 96.02 | 86.90 | 54.61 |
S13 | 印度野橘C. reshni | 109 206 848 | 16 381 027 200 | 103 799 050 | 95.05 | 77.84 | 54.36 |
S14 | 岑溪酸橘 C. reticulata Cenxi Suanju | 109 748 912 | 16 462 336 800 | 104 143 887 | 94.89 | 89.17 | 54.63 |
S15 | 猫儿山野橘C. reticulata Maoershan Yeju | 99 806 304 | 14 970 945 600 | 95 741 594 | 95.93 | 88.23 | 49.68 |
S16 | 沙柑C. nobilis Lour | 109 428 871 | 16 414 330 650 | 105 720 169 | 96.61 | 88.43 | 54.47 |
S17 | 新会橙C. sinensis ‘Xinhuicheng’ | 126 858 264 | 19 028 739 600 | 116 928 159 | 92.17 | 83.69 | 63.14 |
S18 | 沙田柚 C. grandis Shatianyou | 106 098 668 | 15 914 800 200 | 99 741 325 | 94.01 | 80.25 | 52.81 |
S19 | 里斯本柠檬 C. limon Lisbon Lemon | 112 169 164 | 16 825 374 600 | 106 248 936 | 94.72 | 80.82 | 55.83 |
S20 | 广佛手 C. medica Guangfoshou | 116 115 073 | 17 417 260 950 | 110 689 088 | 95.33 | 78.15 | 57.79 |
表3 基因组测序数据及与参考基因组比对结果统计
Table 3 Statistics of genome sequencing and comparison of reference genomes
样品 编号 Sample | 资源 Resource | 总Reads数 Total reads | 总碱基数/bp Total base | 比对Reads数 Comparison reads | 总比对率/% Total ratio | 双端比对率/% Double-terminal ratio | 平均测序深度(×) Average sequencing depth |
---|---|---|---|---|---|---|---|
S01 | 枳Poncirus trifoliata | 107 697 496 | 16 154 624 400 | 99 286 290 | 92.19 | 76.67 | 53.60 |
S02 | 阳朔金柑Fortunella ‘Yangshuo Jingan’ | 89 529 554 | 13 429 433 100 | 83 875 162 | 93.68 | 79.89 | 44.56 |
S03 | 红河大翼橙 Citrus hongheensis | 98 195 835 | 14 729 375 250 | 90 439 245 | 92.10 | 78.80 | 48.88 |
S04 | 龙胜小江村宜昌橙 C. ichangensis ‘Longsheng Xiaojiangcun’ | 109 088 887 | 16 363 333 050 | 103 907 427 | 95.25 | 81.29 | 54.30 |
S05 | 莽山野柑(尖叶) C. mangshanensis (pointed leaf) | 107 753 893 | 16 163 083 950 | 103 036 387 | 95.62 | 81.53 | 53.63 |
S06 | 莽山野柑(圆叶) C. mangshanensis (round leaf) | 103 687 777 | 15 553 166 550 | 99 627 681 | 96.08 | 82.54 | 51.61 |
S07 | 姑婆山野生皱皮柑2号 Guposhan Wild Zhoupigan 2 | 103 255 191 | 15 488 278 650 | 98 252 313 | 95.15 | 81.28 | 51.39 |
S08 | 姑婆山野生皱皮柑5号 Guposhan Wild Zhoupigan 5 | 118 238 006 | 17 735 700 900 | 110 819 337 | 93.73 | 79.74 | 58.85 |
S09 | 姑婆山野生皱皮柑6号 Guposhan Wild Zhoupigan 6 | 92 758 407 | 13 913 761 050 | 85 643 147 | 92.33 | 78.24 | 46.17 |
S10 | 姑婆山野生元橘 Sinocitrus chuana Tseng | 112 921 407 | 16 938 211 050 | 107 256 623 | 94.98 | 81.75 | 56.21 |
S11 | 道县野橘C. daoxianensis | 107 933 335 | 16 190 000 250 | 104 004 963 | 96.36 | 88.68 | 53.72 |
S12 | 立花橘C. tachibana | 109 720 035 | 16 458 005 250 | 105 353 025 | 96.02 | 86.90 | 54.61 |
S13 | 印度野橘C. reshni | 109 206 848 | 16 381 027 200 | 103 799 050 | 95.05 | 77.84 | 54.36 |
S14 | 岑溪酸橘 C. reticulata Cenxi Suanju | 109 748 912 | 16 462 336 800 | 104 143 887 | 94.89 | 89.17 | 54.63 |
S15 | 猫儿山野橘C. reticulata Maoershan Yeju | 99 806 304 | 14 970 945 600 | 95 741 594 | 95.93 | 88.23 | 49.68 |
S16 | 沙柑C. nobilis Lour | 109 428 871 | 16 414 330 650 | 105 720 169 | 96.61 | 88.43 | 54.47 |
S17 | 新会橙C. sinensis ‘Xinhuicheng’ | 126 858 264 | 19 028 739 600 | 116 928 159 | 92.17 | 83.69 | 63.14 |
S18 | 沙田柚 C. grandis Shatianyou | 106 098 668 | 15 914 800 200 | 99 741 325 | 94.01 | 80.25 | 52.81 |
S19 | 里斯本柠檬 C. limon Lisbon Lemon | 112 169 164 | 16 825 374 600 | 106 248 936 | 94.72 | 80.82 | 55.83 |
S20 | 广佛手 C. medica Guangfoshou | 116 115 073 | 17 417 260 950 | 110 689 088 | 95.33 | 78.15 | 57.79 |
样品编号 Sample | 资源 Resource | 位点数 Number of site | 纯合数(%) Homo | 杂合数(%) Hete |
---|---|---|---|---|
S01 | 枳Poncirus trifoliata | 5 342 092 | 4 003 999(74.95) | 1 338 093(25.05) |
S02 | 阳朔金柑Fortunella‘Yangshuo Jingan’ | 4 661 269 | 2 846 563(61.07) | 1 814 706(38.93) |
S03 | 红河大翼橙Citrus hongheensis | 4 165 337 | 2 906 844(69.79) | 1 258 493(30.21) |
S04 | 龙胜小江村宜昌橙C. ichangensis‘Longsheng Xiaojiangcun’ | 3 879 284 | 2 908 068(74.96) | 971 216(25.04) |
S05 | 莽山野柑(尖叶)C. mangshanensis(pointed leaf) | 4 820 706 | 3 348 887(69.47) | 1 471 819(30.53) |
S06 | 莽山野柑(圆叶)C. mangshanensis(round leaf) | 4 841 588 | 3 344 729(69.08) | 1 496 859(30.92) |
S07 | 姑婆山野生皱皮柑2号Guposhan Wild Zhoupigan 2 | 4 738 800 | 3 426 441(72.31) | 1 312 359(27.69) |
S08 | 姑婆山野生皱皮柑5号Guposhan Wild Zhoupigan 5 | 4 840 706 | 3 380 071(69.83) | 1 460 635(30.17) |
S09 | 姑婆山野生皱皮柑6号Guposhan Wild zhoupigan 6 | 4 730 027 | 3 400 590(71.89) | 1 329 437(28.11) |
S10 | 姑婆山野生元橘Sinocitrus chuana Tseng | 4 746 218 | 3 406 565(71.77) | 1 339 653(28.23) |
S11 | 道县野橘C. daoxianensis | 2 254 695 | 988 458(43.84) | 1 266 237(56.16) |
S12 | 立花橘C. tachibana | 2 606 981 | 835 629(32.05) | 1 771 352(67.95) |
S13 | 印度野橘C. reshni | 4 695 910 | 3 771 979(80.32) | 923 931(19.68) |
S14 | 岑溪酸橘C. reticulata Cenxi Suanju | 1 801 567 | 733 504(40.71) | 1 068 063(59.29) |
S15 | 猫儿山野橘C. reticulata Maoershan Yeju | 2 248 710 | 645 918(28.72) | 1 602 792(71.28) |
S16 | 沙柑C. nobilis Lour | 2 688 157 | 379 017(14.10) | 2 309 140(85.90) |
S17 | 新会橙C. sinensis Xinhuicheng | 3 612 044 | 348 953(9.66) | 3 263 091(90.34) |
S18 | 沙田柚C. grandis Shatianyou | 4 225 856 | 2 743 552(64.92) | 1 482 304(35.08) |
S19 | 里斯本柠檬C. limon Lisbon Lemon | 5 537 457 | 1 323 345(23.90) | 4 214 112(76.10) |
S20 | 广佛手C. medica Guangfoshou | 5 149 649 | 3 863 235(75.02) | 1 286 414(24.98) |
表4 20份样本SNP位点检测统计
Table 4 SNP site detection statistics of 20 samples
样品编号 Sample | 资源 Resource | 位点数 Number of site | 纯合数(%) Homo | 杂合数(%) Hete |
---|---|---|---|---|
S01 | 枳Poncirus trifoliata | 5 342 092 | 4 003 999(74.95) | 1 338 093(25.05) |
S02 | 阳朔金柑Fortunella‘Yangshuo Jingan’ | 4 661 269 | 2 846 563(61.07) | 1 814 706(38.93) |
S03 | 红河大翼橙Citrus hongheensis | 4 165 337 | 2 906 844(69.79) | 1 258 493(30.21) |
S04 | 龙胜小江村宜昌橙C. ichangensis‘Longsheng Xiaojiangcun’ | 3 879 284 | 2 908 068(74.96) | 971 216(25.04) |
S05 | 莽山野柑(尖叶)C. mangshanensis(pointed leaf) | 4 820 706 | 3 348 887(69.47) | 1 471 819(30.53) |
S06 | 莽山野柑(圆叶)C. mangshanensis(round leaf) | 4 841 588 | 3 344 729(69.08) | 1 496 859(30.92) |
S07 | 姑婆山野生皱皮柑2号Guposhan Wild Zhoupigan 2 | 4 738 800 | 3 426 441(72.31) | 1 312 359(27.69) |
S08 | 姑婆山野生皱皮柑5号Guposhan Wild Zhoupigan 5 | 4 840 706 | 3 380 071(69.83) | 1 460 635(30.17) |
S09 | 姑婆山野生皱皮柑6号Guposhan Wild zhoupigan 6 | 4 730 027 | 3 400 590(71.89) | 1 329 437(28.11) |
S10 | 姑婆山野生元橘Sinocitrus chuana Tseng | 4 746 218 | 3 406 565(71.77) | 1 339 653(28.23) |
S11 | 道县野橘C. daoxianensis | 2 254 695 | 988 458(43.84) | 1 266 237(56.16) |
S12 | 立花橘C. tachibana | 2 606 981 | 835 629(32.05) | 1 771 352(67.95) |
S13 | 印度野橘C. reshni | 4 695 910 | 3 771 979(80.32) | 923 931(19.68) |
S14 | 岑溪酸橘C. reticulata Cenxi Suanju | 1 801 567 | 733 504(40.71) | 1 068 063(59.29) |
S15 | 猫儿山野橘C. reticulata Maoershan Yeju | 2 248 710 | 645 918(28.72) | 1 602 792(71.28) |
S16 | 沙柑C. nobilis Lour | 2 688 157 | 379 017(14.10) | 2 309 140(85.90) |
S17 | 新会橙C. sinensis Xinhuicheng | 3 612 044 | 348 953(9.66) | 3 263 091(90.34) |
S18 | 沙田柚C. grandis Shatianyou | 4 225 856 | 2 743 552(64.92) | 1 482 304(35.08) |
S19 | 里斯本柠檬C. limon Lisbon Lemon | 5 537 457 | 1 323 345(23.90) | 4 214 112(76.10) |
S20 | 广佛手C. medica Guangfoshou | 5 149 649 | 3 863 235(75.02) | 1 286 414(24.98) |
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