Acta Prataculturae Sinica ›› 2021, Vol. 30 ›› Issue (5): 121-133.DOI: 10.11686/cyxb2020219
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Yi-meng WANG(), Tian-tian MA, Zi-feng OUYANG, Ji-yu ZHANG()
Received:
2020-05-13
Revised:
2020-09-21
Online:
2021-05-20
Published:
2021-04-16
Contact:
Ji-yu ZHANG
Yi-meng WANG, Tian-tian MA, Zi-feng OUYANG, Ji-yu ZHANG. Genome-wide identification of full-length long-terminal repeat retrotransposons and identification of interrupted genes in Cleistogenes songorica[J]. Acta Prataculturae Sinica, 2021, 30(5): 121-133.
超家族 Superfamily | Llorens等[ et al | 参考全长LTR-RTs序列 Reference full-length LTR-RTs | 宿主有机体 Host organism | 无芒隐子草中支系成员数量Number of family members in C. songorica |
---|---|---|---|---|
Copia | Sire | Endovir1 1 | 拟南芥Arabidopsis thaliana | 35 |
SIRE1 4 | 大豆Glycine max | |||
Opie 2 | 水稻Oryza sativa | |||
TSI 9 | 小米Setaria italica | |||
ToRTL 1 | 番茄Solanum lycopersicum | |||
Oryco | Araco | 拟南芥A. thaliana | 138 | |
Vitico1 1 | 葡萄Vitis vitivinifera | |||
Vitico1 2 | 葡萄V. vitivinifera | |||
Retrofit | Koala | 野生稻Oryza australiensis | 83 | |
Retrofit | 长雄野生稻Oryza longistaminata | |||
Hopscotch | 水稻O. sativa | |||
Tork | Sto 4 | 玉米Zea mays | 75 | |
Tnt 1 | 烟草Nicotiana tabacum | |||
V 12 | 葡萄V. vitivinifera | |||
Batata | 红薯Ipomoea batatas | |||
Tto1 | 烟草N. tabacum | |||
RTvr 2 | 绿豆Vigna radiata | |||
Tork 4 | 番茄S. lycopersicum | |||
Gypsy | Athila | Cyclops-2 | 豌豆Pisum sativum | 1 |
Calypso | 大豆G. max | |||
Bagy 2 | 大麦Hordeum vulgare | |||
Athila 4-1 | 拟南芥A. thaliana | |||
Diapsora | 大豆G. max | |||
Tat | Tat 4-1 | 拟南芥A. thaliana | 182 | |
Tf t2 | 拟南芥A. thaliana | |||
RetroSor 1 | 高粱Sorghum bicolor | |||
Cinful 1 | 玉米Z. mays | |||
RIRE 2 | 水稻O. sativa | |||
Ogre | 豌豆P. sativum | |||
Reina | Reina | 玉米Z. mays | 63 | |
Gloin | 拟南芥A. thaliana | |||
Ifg 7 | 辐射松Pinus radiata | |||
Gimli | 拟南芥A. thaliana | |||
CRM | Cereba | 大麦H. vulgare | 47 | |
CRM | 玉米Z. mays | |||
Beetle 1 | 甜菜Beta vulgaris | |||
Galadriel | Monkey | 芭蕉Musabasjoo | 0 | |
Galadriel | 番茄S. lycopersicum | |||
Tntom 1 | 油菜Nicotiana tomentosiformis | |||
Del/Tekay | Tma | 拟南芥A. thaliana | 10 | |
Legolas | 拟南芥A. thaliana | |||
Bagy 1 | 大麦H. vulgare | |||
Retrosat 2 | 水稻O. sativa | |||
Peabody | 豌豆P. sativum | |||
Del | 百合Lilium henryi |
Table 1 Reference full-length LTR-RTs sequences for phylogenetic analysis
超家族 Superfamily | Llorens等[ et al | 参考全长LTR-RTs序列 Reference full-length LTR-RTs | 宿主有机体 Host organism | 无芒隐子草中支系成员数量Number of family members in C. songorica |
---|---|---|---|---|
Copia | Sire | Endovir1 1 | 拟南芥Arabidopsis thaliana | 35 |
SIRE1 4 | 大豆Glycine max | |||
Opie 2 | 水稻Oryza sativa | |||
TSI 9 | 小米Setaria italica | |||
ToRTL 1 | 番茄Solanum lycopersicum | |||
Oryco | Araco | 拟南芥A. thaliana | 138 | |
Vitico1 1 | 葡萄Vitis vitivinifera | |||
Vitico1 2 | 葡萄V. vitivinifera | |||
Retrofit | Koala | 野生稻Oryza australiensis | 83 | |
Retrofit | 长雄野生稻Oryza longistaminata | |||
Hopscotch | 水稻O. sativa | |||
Tork | Sto 4 | 玉米Zea mays | 75 | |
Tnt 1 | 烟草Nicotiana tabacum | |||
V 12 | 葡萄V. vitivinifera | |||
Batata | 红薯Ipomoea batatas | |||
Tto1 | 烟草N. tabacum | |||
RTvr 2 | 绿豆Vigna radiata | |||
Tork 4 | 番茄S. lycopersicum | |||
Gypsy | Athila | Cyclops-2 | 豌豆Pisum sativum | 1 |
Calypso | 大豆G. max | |||
Bagy 2 | 大麦Hordeum vulgare | |||
Athila 4-1 | 拟南芥A. thaliana | |||
Diapsora | 大豆G. max | |||
Tat | Tat 4-1 | 拟南芥A. thaliana | 182 | |
Tf t2 | 拟南芥A. thaliana | |||
RetroSor 1 | 高粱Sorghum bicolor | |||
Cinful 1 | 玉米Z. mays | |||
RIRE 2 | 水稻O. sativa | |||
Ogre | 豌豆P. sativum | |||
Reina | Reina | 玉米Z. mays | 63 | |
Gloin | 拟南芥A. thaliana | |||
Ifg 7 | 辐射松Pinus radiata | |||
Gimli | 拟南芥A. thaliana | |||
CRM | Cereba | 大麦H. vulgare | 47 | |
CRM | 玉米Z. mays | |||
Beetle 1 | 甜菜Beta vulgaris | |||
Galadriel | Monkey | 芭蕉Musabasjoo | 0 | |
Galadriel | 番茄S. lycopersicum | |||
Tntom 1 | 油菜Nicotiana tomentosiformis | |||
Del/Tekay | Tma | 拟南芥A. thaliana | 10 | |
Legolas | 拟南芥A. thaliana | |||
Bagy 1 | 大麦H. vulgare | |||
Retrosat 2 | 水稻O. sativa | |||
Peabody | 豌豆P. sativum | |||
Del | 百合Lilium henryi |
染色 Chromosome | 全长LTR-RTs数 Number of full-length LTR retrotransposons (Copia; Gypsy) | Copia∶Gypsy比率 Ratio of Copia∶Gypsy | 每千万碱基全长LTR-RTs密度 Density of LTR-RTs per 10 million base length (Copia/Gypsy) | 染色体大小 Chromosome size (bp) |
---|---|---|---|---|
Chr1 | 53 (26; 27) | 0.96 | 14.43 (7.08/7.35) | 36730093 |
Chr2 | 54 (26; 28) | 0.93 | 15.37 (7.40/7.97) | 35137460 |
Chr3 | 52 (21; 31) | 0.68 | 15.24 (6.15/9.08) | 34124666 |
Chr4 | 53 (27; 26) | 1.04 | 16.84 (8.58/8.26) | 31471377 |
Chr5 | 53 (24; 29) | 0.83 | 16.71 (7.56/9.14) | 31725061 |
Chr6 | 48 (29; 19) | 1.53 | 15.26 (9.22/2.86) | 31461567 |
Chr7 | 64 (38; 26) | 1.46 | 20.56 (12.21/8.35) | 31124980 |
Chr8 | 42 (30; 12) | 2.50 | 13.91 (9.94/3.98) | 30186489 |
Chr9 | 41 (21; 20) | 1.05 | 15.74 (8.06/7.68) | 26050788 |
Chr10 | 40 (26; 14) | 1.86 | 15.14 (9.84/5.30) | 26425489 |
Chr11 | 39 (17; 22) | 0.77 | 15.39 (6.71/8.68) | 25340727 |
Chr12 | 25 (12; 13) | 0.92 | 12.03 (5.78/6.26) | 20776520 |
Chr13 | 29 (15; 14) | 1.07 | 13.44 (6.95/6.49) | 21572208 |
Chr14 | 31 (20; 11) | 1.82 | 14.64 (9.45/5.20) | 21171528 |
Chr15 | 29 (12; 17) | 0.71 | 14.31 (5.92/8.39) | 20269367 |
Chr16 | 28 (11; 17) | 0.65 | 14.50 (5.70/8.81) | 19304776 |
Chr17 | 31 (14; 17) | 0.82 | 16.47 (7.44/9.03) | 18816966 |
Chr18 | 33 (20; 13) | 1.54 | 17.00 (10.30/6.70) | 19417082 |
Chr19 | 29 (12; 17) | 0.71 | 17.39 (7.20/10.19) | 16677740 |
Chr20 | 20 (12; 8) | 1.50 | 12.16 (7.29/4.86) | 16453899 |
Table 2 Distribution of the identified full-length LTR-RTs on the 20 chromosomes of the C. songorica genome
染色 Chromosome | 全长LTR-RTs数 Number of full-length LTR retrotransposons (Copia; Gypsy) | Copia∶Gypsy比率 Ratio of Copia∶Gypsy | 每千万碱基全长LTR-RTs密度 Density of LTR-RTs per 10 million base length (Copia/Gypsy) | 染色体大小 Chromosome size (bp) |
---|---|---|---|---|
Chr1 | 53 (26; 27) | 0.96 | 14.43 (7.08/7.35) | 36730093 |
Chr2 | 54 (26; 28) | 0.93 | 15.37 (7.40/7.97) | 35137460 |
Chr3 | 52 (21; 31) | 0.68 | 15.24 (6.15/9.08) | 34124666 |
Chr4 | 53 (27; 26) | 1.04 | 16.84 (8.58/8.26) | 31471377 |
Chr5 | 53 (24; 29) | 0.83 | 16.71 (7.56/9.14) | 31725061 |
Chr6 | 48 (29; 19) | 1.53 | 15.26 (9.22/2.86) | 31461567 |
Chr7 | 64 (38; 26) | 1.46 | 20.56 (12.21/8.35) | 31124980 |
Chr8 | 42 (30; 12) | 2.50 | 13.91 (9.94/3.98) | 30186489 |
Chr9 | 41 (21; 20) | 1.05 | 15.74 (8.06/7.68) | 26050788 |
Chr10 | 40 (26; 14) | 1.86 | 15.14 (9.84/5.30) | 26425489 |
Chr11 | 39 (17; 22) | 0.77 | 15.39 (6.71/8.68) | 25340727 |
Chr12 | 25 (12; 13) | 0.92 | 12.03 (5.78/6.26) | 20776520 |
Chr13 | 29 (15; 14) | 1.07 | 13.44 (6.95/6.49) | 21572208 |
Chr14 | 31 (20; 11) | 1.82 | 14.64 (9.45/5.20) | 21171528 |
Chr15 | 29 (12; 17) | 0.71 | 14.31 (5.92/8.39) | 20269367 |
Chr16 | 28 (11; 17) | 0.65 | 14.50 (5.70/8.81) | 19304776 |
Chr17 | 31 (14; 17) | 0.82 | 16.47 (7.44/9.03) | 18816966 |
Chr18 | 33 (20; 13) | 1.54 | 17.00 (10.30/6.70) | 19417082 |
Chr19 | 29 (12; 17) | 0.71 | 17.39 (7.20/10.19) | 16677740 |
Chr20 | 20 (12; 8) | 1.50 | 12.16 (7.29/4.86) | 16453899 |
插入时间 Insertion time (Million years) | 绝对频率 (相对频率) Absolute frequency (relative frequency) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Copia 超家族Superfamily | Gypsy超家族Superfamily | |||||||||
Retrofit | Tork | Sire | Oryco | No cluster | Tat | Reina | CRM | Del | No cluster | |
0~0.5 | 11 (0.13) | 1 (0.01) | 1 (0.03) | 17 (0.12) | 24 (0.23)* | 4 (0.02) | 10 (0.16) | 11 (0.23)* | 1 (0.10) | 37 (0.35)* |
0.5~1.0 | 17 (0.20)* | 6 (0.08) | 6 (0.17) | 24 (0.17) | 16 (0.25)* | 16 (0.09) | 19 (0.30)* | 10 (0.21)* | 1 (0.10) | 10 (0.10) |
1.0~1.5 | 24 (0.29)* | 8 (0.11) | 5 (0.14) | 36 (0.26)* | 25 (0.24)* | 36 (0.20)* | 17 (0.27)* | 10 (0.21)* | 0 (0.00) | 15 (0.14) |
1.5~2.0 | 16 (0.19) | 7 (0.09) | 9 (0.26)* | 30 (0.22)* | 13 (0.13) | 31 (0.17) | 9 (0.14) | 4 (0.09) | 2 (0.20)* | 11 (0.10) |
2.0~2.5 | 9 (0.11) | 14 (0.19) | 7 (0.20)* | 21 (0.15) | 7 (0.07) | 28 (0.15) | 1 (0.02) | 8 (0.17) | 2 (0.20)* | 12 (0.11) |
2.5~3.0 | 3 (0.04) | 13 (0.18) | 3 (0.09) | 5 (0.04) | 6 (0.06) | 24 (0.13) | 2 (0.03) | 2 (0.04) | 1 (0.10) | 8 (0.08) |
3.5~4.0 | 0 (0.00) | 5 (0.07) | 1 (0.03) | 1 (0.01) | 1 (0.01) | 2 (0.01) | 0 (0.00) | 1 (0.02) | 1 (0.10) | 5 (0.05) |
4.0~4.5 | 4 (0.05) | 8 (0.11) | 3 (0.09) | 3 (0.02) | 1 (0.01) | 24 (0.13) | 3 (0.05) | 0 (0.00) | 2 (0.20)* | 5 (0.05) |
4.5~5.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 1 (0.01) | 0 (0.00) | 2 (0.01) | 1 (0.02) | 0 (0.00) | 0 (0.00) | 1 (0.01) |
5.0~5.5 | 0 (0.00) | 4 (0.05) | 0 (0.00) | 0 (0.00) | 1 (0.01) | 1 (0.01) | 1 (0.02) | 1 (0.02) | 0 (0.00) | 0 (0.00) |
5.5~6.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
6.0~6.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
6.5~7.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
7.0~7.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
7.5~8.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
3.0~3.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 1 (0.01) |
Table 3 Estimated insertion times of different lineages of full-length Copia and Gypsy superfamily members in C. songorica
插入时间 Insertion time (Million years) | 绝对频率 (相对频率) Absolute frequency (relative frequency) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Copia 超家族Superfamily | Gypsy超家族Superfamily | |||||||||
Retrofit | Tork | Sire | Oryco | No cluster | Tat | Reina | CRM | Del | No cluster | |
0~0.5 | 11 (0.13) | 1 (0.01) | 1 (0.03) | 17 (0.12) | 24 (0.23)* | 4 (0.02) | 10 (0.16) | 11 (0.23)* | 1 (0.10) | 37 (0.35)* |
0.5~1.0 | 17 (0.20)* | 6 (0.08) | 6 (0.17) | 24 (0.17) | 16 (0.25)* | 16 (0.09) | 19 (0.30)* | 10 (0.21)* | 1 (0.10) | 10 (0.10) |
1.0~1.5 | 24 (0.29)* | 8 (0.11) | 5 (0.14) | 36 (0.26)* | 25 (0.24)* | 36 (0.20)* | 17 (0.27)* | 10 (0.21)* | 0 (0.00) | 15 (0.14) |
1.5~2.0 | 16 (0.19) | 7 (0.09) | 9 (0.26)* | 30 (0.22)* | 13 (0.13) | 31 (0.17) | 9 (0.14) | 4 (0.09) | 2 (0.20)* | 11 (0.10) |
2.0~2.5 | 9 (0.11) | 14 (0.19) | 7 (0.20)* | 21 (0.15) | 7 (0.07) | 28 (0.15) | 1 (0.02) | 8 (0.17) | 2 (0.20)* | 12 (0.11) |
2.5~3.0 | 3 (0.04) | 13 (0.18) | 3 (0.09) | 5 (0.04) | 6 (0.06) | 24 (0.13) | 2 (0.03) | 2 (0.04) | 1 (0.10) | 8 (0.08) |
3.5~4.0 | 0 (0.00) | 5 (0.07) | 1 (0.03) | 1 (0.01) | 1 (0.01) | 2 (0.01) | 0 (0.00) | 1 (0.02) | 1 (0.10) | 5 (0.05) |
4.0~4.5 | 4 (0.05) | 8 (0.11) | 3 (0.09) | 3 (0.02) | 1 (0.01) | 24 (0.13) | 3 (0.05) | 0 (0.00) | 2 (0.20)* | 5 (0.05) |
4.5~5.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 1 (0.01) | 0 (0.00) | 2 (0.01) | 1 (0.02) | 0 (0.00) | 0 (0.00) | 1 (0.01) |
5.0~5.5 | 0 (0.00) | 4 (0.05) | 0 (0.00) | 0 (0.00) | 1 (0.01) | 1 (0.01) | 1 (0.02) | 1 (0.02) | 0 (0.00) | 0 (0.00) |
5.5~6.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
6.0~6.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
6.5~7.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
7.0~7.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
7.5~8.0 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) |
3.0~3.5 | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 0 (0.00) | 1 (0.01) |
基因ID Gene ID | GO功能 GO function | LR | LS | HR | HS | RR | RS | NS | NR |
---|---|---|---|---|---|---|---|---|---|
CCG009101 | 蛋白泛素化参与泛素依赖性蛋白的分解代谢过程Protein ubiquitination involved in ubiquitin-dependent protein catabolic process | 2.67 | 2.11 | 0.99 | 0.72 | 0.93 | 1.86 | 3.215205 | 3.137421 |
CCG009854 | 激活脱落酸的信号通路Abscisic acid-activated signaling pathway | 0.28 | 1.20 | 0.34 | 0.14 | 0.31 | 0.15 | 3.195202 | 8.035544 |
CCG016150 | 光周期Photoperiodism | 0.03 | 0.93 | 0.03 | 0.07 | 0.08 | 0.05 | 4.634620 | 6.481022 |
CCG020579 | DNA复制DNA replication | 3.37 | 1.98 | 3.37 | 8.45 | 11.06 | 1.40 | 0.649759 | 3.584700 |
CCG031250 | 肽酶活性Peptidase activity | 0.72 | 0.66 | 0.04 | 0.10 | 0.24 | 0.10 | 0.016040 | 0.059849 |
CCG032101 | 刺激应答Response to stimulus | 0.19 | 0.76 | 0.72 | 0.66 | 0.04 | 0.10 | 3.645388 | 4.949373 |
CCG035285 | 氧化还原酶活性Oxidoreductase activity | 0.62 | 0.26 | 0.03 | 0.19 | 0.25 | 0.23 | 0.111286 | 0.333672 |
CCG041800 | 内质网到高尔基囊泡的转运ER to Golgi vesicle-mediated transport | 0.23 | 0.64 | 0.15 | 0.13 | 0.20 | 0.20 | 6.572815 | 12.440860 |
CCG048604 | 甘油代谢过程Glycerol metabolic process | 1.99 | 0.95 | 4.11 | 2.95 | 4.75 | 0.80 | 3.265621 | 4.571146 |
CCG052980 | 核质运输Nucleocytoplasmic transport | 1.28 | 0.27 | 0.58 | 0.25 | 0.64 | 0.32 | 0.170547 | 0.517852 |
Table 4 GO functions of 10 interrupted genes and expression under drought stress and rehydration in C. songorica (FPKM)
基因ID Gene ID | GO功能 GO function | LR | LS | HR | HS | RR | RS | NS | NR |
---|---|---|---|---|---|---|---|---|---|
CCG009101 | 蛋白泛素化参与泛素依赖性蛋白的分解代谢过程Protein ubiquitination involved in ubiquitin-dependent protein catabolic process | 2.67 | 2.11 | 0.99 | 0.72 | 0.93 | 1.86 | 3.215205 | 3.137421 |
CCG009854 | 激活脱落酸的信号通路Abscisic acid-activated signaling pathway | 0.28 | 1.20 | 0.34 | 0.14 | 0.31 | 0.15 | 3.195202 | 8.035544 |
CCG016150 | 光周期Photoperiodism | 0.03 | 0.93 | 0.03 | 0.07 | 0.08 | 0.05 | 4.634620 | 6.481022 |
CCG020579 | DNA复制DNA replication | 3.37 | 1.98 | 3.37 | 8.45 | 11.06 | 1.40 | 0.649759 | 3.584700 |
CCG031250 | 肽酶活性Peptidase activity | 0.72 | 0.66 | 0.04 | 0.10 | 0.24 | 0.10 | 0.016040 | 0.059849 |
CCG032101 | 刺激应答Response to stimulus | 0.19 | 0.76 | 0.72 | 0.66 | 0.04 | 0.10 | 3.645388 | 4.949373 |
CCG035285 | 氧化还原酶活性Oxidoreductase activity | 0.62 | 0.26 | 0.03 | 0.19 | 0.25 | 0.23 | 0.111286 | 0.333672 |
CCG041800 | 内质网到高尔基囊泡的转运ER to Golgi vesicle-mediated transport | 0.23 | 0.64 | 0.15 | 0.13 | 0.20 | 0.20 | 6.572815 | 12.440860 |
CCG048604 | 甘油代谢过程Glycerol metabolic process | 1.99 | 0.95 | 4.11 | 2.95 | 4.75 | 0.80 | 3.265621 | 4.571146 |
CCG052980 | 核质运输Nucleocytoplasmic transport | 1.28 | 0.27 | 0.58 | 0.25 | 0.64 | 0.32 | 0.170547 | 0.517852 |
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