Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (5): 958-972.doi: 10.16420/j.issn.0513-353x.2021-0103
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LIANG Qin1,2, ZHANG Yanhui3, KANG Kaiquan4, LIU Jinhang1, LI Liang1, FENG Yu1, WANG Chao1, YANG Chao1,*(), LI Yongyu1,*(
)
Received:
2022-01-11
Revised:
2022-04-01
Online:
2022-05-25
Published:
2022-05-25
Contact:
YANG Chao,LI Yongyu
E-mail:yycc32@126.com;lilin3182@163.com
CLC Number:
LIANG Qin, ZHANG Yanhui, KANG Kaiquan, LIU Jinhang, LI Liang, FENG Yu, WANG Chao, YANG Chao, LI Yongyu. Molecular Evolution of MiR168 Family and Their Expression Profiling During Dormancy of Pyrus pyrifolia[J]. Acta Horticulturae Sinica, 2022, 49(5): 958-972.
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URL: https://www.ahs.ac.cn/EN/10.16420/j.issn.0513-353x.2021-0103
用途Purpose | 引物名称Primer name | 引物序列(5′-3′)Primer sequence |
---|---|---|
克隆Clone | ppy-miR168a-F | ATAGAGGCGTAGGCCTGTGT |
ppy-miR168a-R | TGATGGTGGGAATTGGGATAT | |
克隆Clone | ppy-miR168b-F | TGTCTGTTTGGGCGTTGATT |
ppy-miR168b-R | AAACTATTGTAGATCAGACAACAACGC | |
qRT-PCR | Ppy-miR168a | TCGCTTGGTGCAGGTCG |
AGO1-F | CACCAGCACCACAACAATA | |
AGO1-R | ACCACCACCATAGCCTCT | |
CalS3-F | AGAGGCGGATAACTCG | |
CalS3-R | GCAACACGAAGAATGG | |
Actin-F | CCATCCAGGCTGTTCTCTC | |
Actin-R | GCAAGGTCCAGACGAAGG | |
5SrRNA-F | TAGGCGTAGAGGAACCACACCAAT | |
5SrRNA-R | ACAGTATCGTCACCGCAGTAGAGT |
Table 1 The primers used in this experiment
用途Purpose | 引物名称Primer name | 引物序列(5′-3′)Primer sequence |
---|---|---|
克隆Clone | ppy-miR168a-F | ATAGAGGCGTAGGCCTGTGT |
ppy-miR168a-R | TGATGGTGGGAATTGGGATAT | |
克隆Clone | ppy-miR168b-F | TGTCTGTTTGGGCGTTGATT |
ppy-miR168b-R | AAACTATTGTAGATCAGACAACAACGC | |
qRT-PCR | Ppy-miR168a | TCGCTTGGTGCAGGTCG |
AGO1-F | CACCAGCACCACAACAATA | |
AGO1-R | ACCACCACCATAGCCTCT | |
CalS3-F | AGAGGCGGATAACTCG | |
CalS3-R | GCAACACGAAGAATGG | |
Actin-F | CCATCCAGGCTGTTCTCTC | |
Actin-R | GCAAGGTCCAGACGAAGG | |
5SrRNA-F | TAGGCGTAGAGGAACCACACCAAT | |
5SrRNA-R | ACAGTATCGTCACCGCAGTAGAGT |
科 Family | 物种 Species | 简写 Logogram | miR168数量 Quantity of miR168 | pre-miR168数量 Quantity of pre-miR168 |
---|---|---|---|---|
十字花科Brassicaceae | 拟南芥Arabidopsis thaliana | ath | 4 | 2 |
油菜Brassica napus | bna | 2 | 2 | |
琴叶拟南芥Arabidopsis lyrata | aly | 4 | 2 | |
芜菁Brassica rapa | bra | 6 | 3 | |
亚麻荠Camelina sativa | csa | 1 | 1 | |
禾本科Poaceae | 青稞Hordeum vulgare | hvu | 2 | 1 |
二穗短柄草Brachypodium distachyon | bdi | 2 | 1 | |
甘蔗属Saccharum sp | ssp | 1 | 1 | |
甘蔗Saccharum officinarum | sof | 2 | 2 | |
水稻Oryza sativa | osa | 3 | 2 | |
高粱Sorghum bicolor | sbi | 1 | 1 | |
玉米Zea mays | zma | 4 | 2 | |
山羊草Aegilops tauschii | ata | 1 | 1 | |
豆科Leguminosae | 大豆Glycine max | gma | 2 | 2 |
蒺藜苜蓿Medicago truncatula | mtr | 4 | 3 | |
大叶相思Acacia auriculiformis | aau | 1 | 1 | |
豇豆Vigna unguiculata | vun | 1 | 1 | |
百脉根Lotus japonicus | lja | 1 | 1 | |
科 Family | 物种 Species | 简写 Logogram | miR168数量 Quantity of miR168 | pre-miR168数量 Quantity of pre-miR168 |
杨柳科Salicaceae Mirb | 毛果杨Populus trichocarpa | ptc | 4 | 2 |
葡萄科Vitaceae Juss | 葡萄Vitis vinifera | vvi | 1 | 1 |
毛茛科Ranunculaceae Juss | 耧斗菜Aquilegia viridiflora | aqc | 1 | 1 |
芸香科Rutaceae Juss | 脐橙Citrus sinensis | csi | 2 | 1 |
柑橘Citrus reticulata | cre | 1 | 1 | |
克萊门柚Citrus clementina | ccl | 1 | 1 | |
大戟科Rosaceae Juss | 木薯Manihot esculenta | mes | 1 | 1 |
三叶橡胶树 Hevea brasiliensis | hbr | 1 | 1 | |
蓖麻 Ricinus communis | rco | 1 | 1 | |
葫芦科Cucurbitaceae | 甜瓜Cucumis melo | cme | 1 | 1 |
菊科Asteraceae Bercht | 刺苞菜蓟Cynara cardunculus | cca | 1 | 1 |
亚麻科Linaceae | 亚麻Linum usitatissimum | lus | 2 | 2 |
茄科Solanaceae Juss | 烟草Nicotiana tabacum | nta | 5 | 5 |
番茄Lycopersicon esculentum | sly | 4 | 2 | |
蔷薇科Rosaceae Juss | 苹果Malus domestica | mdm | 2 | 2 |
碧桃Prunus persica | ppe | 1 | 1 | |
森林草莓Fragaria vesca | fve | 1 | 1 | |
凤梨科Bromeliaceae Juss | 莺歌凤梨Vriesea carinata | vcr | 4 | 2 |
松科Pinaceae Lindl | 挪威云杉Picea abies | pab | 2 | 2 |
百合科Liliaceae Juss | 芦笋Asparagus officinalis | aof | 2 | 2 |
梧桐科Sterculiaceae | 可可Theobroma cacao | tcc | 1 | 1 |
Table 2 Distribution and quantity of plant miR168 family members
科 Family | 物种 Species | 简写 Logogram | miR168数量 Quantity of miR168 | pre-miR168数量 Quantity of pre-miR168 |
---|---|---|---|---|
十字花科Brassicaceae | 拟南芥Arabidopsis thaliana | ath | 4 | 2 |
油菜Brassica napus | bna | 2 | 2 | |
琴叶拟南芥Arabidopsis lyrata | aly | 4 | 2 | |
芜菁Brassica rapa | bra | 6 | 3 | |
亚麻荠Camelina sativa | csa | 1 | 1 | |
禾本科Poaceae | 青稞Hordeum vulgare | hvu | 2 | 1 |
二穗短柄草Brachypodium distachyon | bdi | 2 | 1 | |
甘蔗属Saccharum sp | ssp | 1 | 1 | |
甘蔗Saccharum officinarum | sof | 2 | 2 | |
水稻Oryza sativa | osa | 3 | 2 | |
高粱Sorghum bicolor | sbi | 1 | 1 | |
玉米Zea mays | zma | 4 | 2 | |
山羊草Aegilops tauschii | ata | 1 | 1 | |
豆科Leguminosae | 大豆Glycine max | gma | 2 | 2 |
蒺藜苜蓿Medicago truncatula | mtr | 4 | 3 | |
大叶相思Acacia auriculiformis | aau | 1 | 1 | |
豇豆Vigna unguiculata | vun | 1 | 1 | |
百脉根Lotus japonicus | lja | 1 | 1 | |
科 Family | 物种 Species | 简写 Logogram | miR168数量 Quantity of miR168 | pre-miR168数量 Quantity of pre-miR168 |
杨柳科Salicaceae Mirb | 毛果杨Populus trichocarpa | ptc | 4 | 2 |
葡萄科Vitaceae Juss | 葡萄Vitis vinifera | vvi | 1 | 1 |
毛茛科Ranunculaceae Juss | 耧斗菜Aquilegia viridiflora | aqc | 1 | 1 |
芸香科Rutaceae Juss | 脐橙Citrus sinensis | csi | 2 | 1 |
柑橘Citrus reticulata | cre | 1 | 1 | |
克萊门柚Citrus clementina | ccl | 1 | 1 | |
大戟科Rosaceae Juss | 木薯Manihot esculenta | mes | 1 | 1 |
三叶橡胶树 Hevea brasiliensis | hbr | 1 | 1 | |
蓖麻 Ricinus communis | rco | 1 | 1 | |
葫芦科Cucurbitaceae | 甜瓜Cucumis melo | cme | 1 | 1 |
菊科Asteraceae Bercht | 刺苞菜蓟Cynara cardunculus | cca | 1 | 1 |
亚麻科Linaceae | 亚麻Linum usitatissimum | lus | 2 | 2 |
茄科Solanaceae Juss | 烟草Nicotiana tabacum | nta | 5 | 5 |
番茄Lycopersicon esculentum | sly | 4 | 2 | |
蔷薇科Rosaceae Juss | 苹果Malus domestica | mdm | 2 | 2 |
碧桃Prunus persica | ppe | 1 | 1 | |
森林草莓Fragaria vesca | fve | 1 | 1 | |
凤梨科Bromeliaceae Juss | 莺歌凤梨Vriesea carinata | vcr | 4 | 2 |
松科Pinaceae Lindl | 挪威云杉Picea abies | pab | 2 | 2 |
百合科Liliaceae Juss | 芦笋Asparagus officinalis | aof | 2 | 2 |
梧桐科Sterculiaceae | 可可Theobroma cacao | tcc | 1 | 1 |
Fig. 3 Evolutionary tree of miR168(a)and multiple sequences comparison(b) ath. Arabidopsis thaliana;ptc. Populus trichocarpa;vvi. Vitis vinifera;crt. Citrus reticulata;csi. Citrus sinensis;mdm. Malus × domestica;ppe. Prunus persica;fve. Fragaria vesca.
Fig. 5 Analysis of secondary stem-loop structure of Pyrus pyrifolia miR168 precursors. The redder the color,the more likely the base is to be in a pair,and vice versa.
靶基因注释 Target gene annotation | 靶基因编号 Target accession | 期望值 Expection |
---|---|---|
AGO1蛋白 Protein argonaute 1-like transcript variant | XM_018645622.1 | 0 |
XM_018647395.1 | 0 | |
XM_009349800.2 | 0 | |
XM_018645623.1 | 0 | |
XM_018647396.1 | 0 | |
XM_009357682.2 | 0 | |
胼胝质合成酶3(CalS3) Callose synthase 3(CalS3)transcript variant | XM_018649103.1 | 2.5 |
XM_009376827.2 | 2.5 | |
XM_018651590.1 | 2.5 | |
XM_018651591.1 | 2.5 | |
XM_009365800.2 | 2.5 | |
XM_018649104.1 | 2.5 | |
XM_009365801.2 | 2.5 | |
XM_009365802.2 | 2.5 | |
XM_009365803.2 | 2.5 | |
AGO1蛋白Protein argonaute 1-like transcript variant | XM_009359066.2 | 2.5 |
XM_009349798.2 | 2.5 | |
XM_009359065.2 | 2.5 | |
XM_009349797.2 | 2.5 | |
XM_009357684.2 | 2.5 | |
XM_009357683.2 | 2.5 |
Table 3 Target genes prediction of pear miR168 family(ppy-miR168a-5p,ppy-miR168,ppy-miR168b)
靶基因注释 Target gene annotation | 靶基因编号 Target accession | 期望值 Expection |
---|---|---|
AGO1蛋白 Protein argonaute 1-like transcript variant | XM_018645622.1 | 0 |
XM_018647395.1 | 0 | |
XM_009349800.2 | 0 | |
XM_018645623.1 | 0 | |
XM_018647396.1 | 0 | |
XM_009357682.2 | 0 | |
胼胝质合成酶3(CalS3) Callose synthase 3(CalS3)transcript variant | XM_018649103.1 | 2.5 |
XM_009376827.2 | 2.5 | |
XM_018651590.1 | 2.5 | |
XM_018651591.1 | 2.5 | |
XM_009365800.2 | 2.5 | |
XM_018649104.1 | 2.5 | |
XM_009365801.2 | 2.5 | |
XM_009365802.2 | 2.5 | |
XM_009365803.2 | 2.5 | |
AGO1蛋白Protein argonaute 1-like transcript variant | XM_009359066.2 | 2.5 |
XM_009349798.2 | 2.5 | |
XM_009359065.2 | 2.5 | |
XM_009349797.2 | 2.5 | |
XM_009357684.2 | 2.5 | |
XM_009357683.2 | 2.5 |
处理日期(M-D)Treatment date | ppy-miR168a | AGO1 | CalS3 |
---|---|---|---|
11-01 | 0.22 | 0 | 4.00 |
11-25 | 3.37 | 0.05 | 1.03 |
12-27 | 1.12 | 0.58 | 0.75 |
01-23 | 1.00 | 5.91 | 0.59 |
相关系数Correlation coefficient | -0.223 | -0.503 |
Table 4 Correlation analysis of ppy-miR168a and its target genes expression
处理日期(M-D)Treatment date | ppy-miR168a | AGO1 | CalS3 |
---|---|---|---|
11-01 | 0.22 | 0 | 4.00 |
11-25 | 3.37 | 0.05 | 1.03 |
12-27 | 1.12 | 0.58 | 0.75 |
01-23 | 1.00 | 5.91 | 0.59 |
相关系数Correlation coefficient | -0.223 | -0.503 |
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