植物学报 ›› 2019, Vol. 54 ›› Issue (3): 316-327.DOI: 10.11983/CBB18176
收稿日期:
2018-08-14
接受日期:
2018-12-10
出版日期:
2019-07-01
发布日期:
2019-11-24
通讯作者:
杨若林
基金资助:
Received:
2018-08-14
Accepted:
2018-12-10
Online:
2019-07-01
Published:
2019-11-24
Contact:
Ruolin Yang
摘要:
物种基因组成是一个高度动态的进化过程, 其中相对较近起源的种系和物种特异性基因会持续整合到包含古老基因的原始基因网络中。新基因在塑造基因组结构中发挥重要作用, 能提高物种适应性。基因复制和新基因的从头起源是产生新基因及改变基因家族大小的2种方式。目前, 大豆(Glycine max)基因起源时间与进化模式的相互联系很大程度上还未被探索。该研究选择19种具有代表性的被子植物基因组, 分析基因含量动态性与大豆基因起源之间的潜在联系。采用基因出现法, 研究显示约58.7%的大豆基因能追溯到大约1.5亿年前, 同时有21.7%的基因为最近起源的orphan基因。研究结果表明, 与新基因相比, 古老基因受到更强的负选择压并且更加保守。此外, 古老基因的表达水平更高且更可能发生选择性剪切。此外, 具有不同拷贝数的基因在上述特征中也具有明显差异。研究结果有助于认识不同年龄基因的进化模式。
唐康,杨若林. 大豆蛋白编码基因起源与进化. 植物学报, 2019, 54(3): 316-327.
Kang Tang,Ruolin Yang. Origin and Evolution of Soybean Protein-coding Genes. Chinese Bulletin of Botany, 2019, 54(3): 316-327.
图1 19种被子植物基因家族大小分布(A) 系统发育树代表19种被子植物的进化关系; (B) 直系同源基因家族大小; (C) orphan基因家族大小。白、灰、黑分别代表单拷贝、两拷贝和多拷贝基因所占比例。
Figure 1 Gene family size distribution of 19 angiosperm species(A) Phylogenetic tree showing the relationships between the 19 angiosperm species used in this study; (B) Homologous gene family sizes; (C) Gene family sizes of orphan genes. The colors indicate the proportions of genes, white for singletons, grey for two-genes and black for multigenes.
Species | Singletons | Two-gene families | Multigene families | Total gene families | Maximum gene family size |
---|---|---|---|---|---|
Amborella trichopoda | 9823 | 1061(2122) | 523(2935) | 11407 | 207 |
Ananas comosus | 9059 | 2087(4174) | 1007(4916) | 12153 | 124 |
Oryza sativa | 11966 | 2269(4538) | 1167(5805) | 15402 | 64 |
Brachypodium distachyon | 11455 | 2264(4528) | 1209(6066) | 14928 | 50 |
Sorghum bicolor | 12663 | 2529(5058) | 1399(8749) | 16591 | 416 |
Zea mays | 10277 | 3568(7136) | 1964(10539) | 15809 | 297 |
Solanum tuberosum | 11592 | 2390(4780) | 1399(10741) | 15381 | 1051 |
S. lycopersicum | 12210 | 2448(4896) | 1371(7277) | 16029 | 72 |
Vitis vinifera | 10408 | 1931(3862) | 1104(6483) | 13443 | 100 |
Populus trichocarpa | 6550 | 5476(10952) | 2337(13368) | 14363 | 108 |
Gossypium raimondii | 7582 | 3700(7400) | 2960(14806) | 14242 | 90 |
Carica papaya | 10776 | 1505(3010) | 667(3948) | 12948 | 194 |
Arabidopsis thaliana | 13278 | 2485(4970) | 1194(6144) | 16957 | 125 |
A. lyrata | 12767 | 2605(5210) | 1327(6596) | 16699 | 67 |
Cucumis sativus | 10152 | 1691(3382) | 795(4038) | 12638 | 38 |
Prunus persica | 10822 | 1876(3752) | 1106(7192) | 13804 | 217 |
Medicago truncatula | 9936 | 2812(5624) | 1948(13673) | 14696 | 308 |
Glycine max | 4241 | 7735(15470) | 4206(23027) | 16182 | 153 |
Phaseolus vulgaris | 11324 | 2873(5746) | 1430(7626) | 15569 | 132 |
表1 19种被子植物中直系同源基因家族(及基因)数目
Table 1 Number of homologous gene families (and genes) in 19 angiosperm species
Species | Singletons | Two-gene families | Multigene families | Total gene families | Maximum gene family size |
---|---|---|---|---|---|
Amborella trichopoda | 9823 | 1061(2122) | 523(2935) | 11407 | 207 |
Ananas comosus | 9059 | 2087(4174) | 1007(4916) | 12153 | 124 |
Oryza sativa | 11966 | 2269(4538) | 1167(5805) | 15402 | 64 |
Brachypodium distachyon | 11455 | 2264(4528) | 1209(6066) | 14928 | 50 |
Sorghum bicolor | 12663 | 2529(5058) | 1399(8749) | 16591 | 416 |
Zea mays | 10277 | 3568(7136) | 1964(10539) | 15809 | 297 |
Solanum tuberosum | 11592 | 2390(4780) | 1399(10741) | 15381 | 1051 |
S. lycopersicum | 12210 | 2448(4896) | 1371(7277) | 16029 | 72 |
Vitis vinifera | 10408 | 1931(3862) | 1104(6483) | 13443 | 100 |
Populus trichocarpa | 6550 | 5476(10952) | 2337(13368) | 14363 | 108 |
Gossypium raimondii | 7582 | 3700(7400) | 2960(14806) | 14242 | 90 |
Carica papaya | 10776 | 1505(3010) | 667(3948) | 12948 | 194 |
Arabidopsis thaliana | 13278 | 2485(4970) | 1194(6144) | 16957 | 125 |
A. lyrata | 12767 | 2605(5210) | 1327(6596) | 16699 | 67 |
Cucumis sativus | 10152 | 1691(3382) | 795(4038) | 12638 | 38 |
Prunus persica | 10822 | 1876(3752) | 1106(7192) | 13804 | 217 |
Medicago truncatula | 9936 | 2812(5624) | 1948(13673) | 14696 | 308 |
Glycine max | 4241 | 7735(15470) | 4206(23027) | 16182 | 153 |
Phaseolus vulgaris | 11324 | 2873(5746) | 1430(7626) | 15569 | 132 |
Species | Singletons | Two-gene families | Multigene families | Species-specific genes | Maximum gene family size |
---|---|---|---|---|---|
Amborella trichopoda | 7892 | 547(1094) | 502(3447) | 12433 | 105 |
Ananas comosus | 5685 | 483(966) | 297(2224) | 8875 | 94 |
Oryza sativa | 10774 | 686(1372) | 292(1224) | 13370 | 29 |
Brachypodium distachyon | 3485 | 235(470) | 125(548) | 4503 | 15 |
Sorghum bicolor | 5682 | 350(700) | 254(1644) | 8026 | 103 |
Zea mays | 7253 | 813(1626) | 552(2643) | 11522 | 65 |
Solanum tuberosum | 7278 | 471(942) | 376(3688) | 11908 | 163 |
S. lycopersicum | 7836 | 308(616) | 177(950) | 9402 | 51 |
Vitis vinifera | 7238 | 445(890) | 229(1006) | 9134 | 44 |
Populus trichocarpa | 7923 | 593(1186) | 281(1398) | 10507 | 31 |
Gossypium raimondii | 5495 | 408(816) | 293(1406) | 7717 | 26 |
Carica papaya | 7680 | 307(614) | 224(1653) | 9947 | 88 |
Arabidopsis thaliana | 2751 | 105(210) | 57(261) | 3222 | 21 |
A. lyrata | 5413 | 461(922) | 366(1759) | 8094 | 83 |
Cucumis sativus | 3458 | 125(250) | 54(223) | 3931 | 13 |
Prunus persica | 3347 | 242(484) | 195(2483) | 6314 | 838 |
Medicago truncatula | 12763 | 962(1924) | 820(6524) | 21211 | 145 |
Glycine max | 9961 | 476(952) | 118(523) | 11436 | 23 |
Phaseolus vulgaris | 2013 | 85(170) | 58(318) | 2501 | 19 |
表2 19种被子植物中的orphan基因家族(及基因)数目
Table 2 Number of orphan gene families (and genes) in 19 angiosperm species
Species | Singletons | Two-gene families | Multigene families | Species-specific genes | Maximum gene family size |
---|---|---|---|---|---|
Amborella trichopoda | 7892 | 547(1094) | 502(3447) | 12433 | 105 |
Ananas comosus | 5685 | 483(966) | 297(2224) | 8875 | 94 |
Oryza sativa | 10774 | 686(1372) | 292(1224) | 13370 | 29 |
Brachypodium distachyon | 3485 | 235(470) | 125(548) | 4503 | 15 |
Sorghum bicolor | 5682 | 350(700) | 254(1644) | 8026 | 103 |
Zea mays | 7253 | 813(1626) | 552(2643) | 11522 | 65 |
Solanum tuberosum | 7278 | 471(942) | 376(3688) | 11908 | 163 |
S. lycopersicum | 7836 | 308(616) | 177(950) | 9402 | 51 |
Vitis vinifera | 7238 | 445(890) | 229(1006) | 9134 | 44 |
Populus trichocarpa | 7923 | 593(1186) | 281(1398) | 10507 | 31 |
Gossypium raimondii | 5495 | 408(816) | 293(1406) | 7717 | 26 |
Carica papaya | 7680 | 307(614) | 224(1653) | 9947 | 88 |
Arabidopsis thaliana | 2751 | 105(210) | 57(261) | 3222 | 21 |
A. lyrata | 5413 | 461(922) | 366(1759) | 8094 | 83 |
Cucumis sativus | 3458 | 125(250) | 54(223) | 3931 | 13 |
Prunus persica | 3347 | 242(484) | 195(2483) | 6314 | 838 |
Medicago truncatula | 12763 | 962(1924) | 820(6524) | 21211 | 145 |
Glycine max | 9961 | 476(952) | 118(523) | 11436 | 23 |
Phaseolus vulgaris | 2013 | 85(170) | 58(318) | 2501 | 19 |
Phylostratum internode | Genes (%) | Singletons | Two-genes | Multigenes |
---|---|---|---|---|
Angiosperm (PS1) | 30932(58.7%) | 1982 | 5150(10300) | 3400(18650) |
Mesangiosperm (PS2) | 4057(7.7%) | 508 | 708(1416) | 359(2133) |
Eudicot (PS3) | 2356(4.5%) | 303 | 521(1042) | 206(1011) |
Rosid (PS4) | 582(1.1%) | 109 | 181(362) | 31(111) |
Legume (PS5) | 1780(3.4%) | 460 | 452(904) | 87(416) |
Phaseoleae (PS6) | 1590(3.0%) | 568 | 400(800) | 49(222) |
Soybean (PS7) | 11436(21.7%) | 9961 | 476(952) | 118(523) |
表3 定位到每个系统发育层级的大豆基因家族(和基因)数目
Table 3 Number of soybean gene families (and genes) assigned to each phylostratum
Phylostratum internode | Genes (%) | Singletons | Two-genes | Multigenes |
---|---|---|---|---|
Angiosperm (PS1) | 30932(58.7%) | 1982 | 5150(10300) | 3400(18650) |
Mesangiosperm (PS2) | 4057(7.7%) | 508 | 708(1416) | 359(2133) |
Eudicot (PS3) | 2356(4.5%) | 303 | 521(1042) | 206(1011) |
Rosid (PS4) | 582(1.1%) | 109 | 181(362) | 31(111) |
Legume (PS5) | 1780(3.4%) | 460 | 452(904) | 87(416) |
Phaseoleae (PS6) | 1590(3.0%) | 568 | 400(800) | 49(222) |
Soybean (PS7) | 11436(21.7%) | 9961 | 476(952) | 118(523) |
图2 大豆基因起源(A) 不同起源节点(PS1-PS7)基因数目; (B) 基因比例; (C) 基因拷贝数状态; (D) 基因GO注释
Figure 2 Origination of soybean genes(A) Numbers in parenthesis denote the number of genes per phylostratum (PS1-PS7); (B) Gene fraction; (C) Gene copy status; (D) Gene Ontology annotation
图3 大豆基因分歧程度通过大豆与菜豆同源基因对来评估选择压(dN/dS)(A)、同义替换率(dS) (B)和非同义替换率(dN) (C)。
Figure 3 Divergence degrees of soybean genes Estimated between soybean and common bean selection pressure (dN/dS)(A), synonymous substitution rate (dS) (B) and nonsynonymous substitution rate (dN) (C).
图5 大豆基因的选择性剪切(AS)(A) 选择性剪切事件; (B) 发生选择性剪切的基因比例; (C) 不同拷贝数状态下发生选择性剪切的基因; (D) 每个基因发生选择性剪切事件的数目
Figure 5 Alternative splicing (AS) of soybean genes(A) AS event; (B) AS genes ratio; (C) AS genes for different copy status; (D) AS number per gene
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