园艺学报 ›› 2023, Vol. 50 ›› Issue (3): 523-533.doi: 10.16420/j.issn.0513-353x.2021-1196
收稿日期:
2022-04-18
修回日期:
2022-10-03
出版日期:
2023-03-25
发布日期:
2023-04-03
通讯作者:
*(E-mail:guodalong@haust.edu.cn)
基金资助:
MA Shuaihui, HE Guangqi, CHENG Yizhe, GUO Dalong*()
Received:
2022-04-18
Revised:
2022-10-03
Online:
2023-03-25
Published:
2023-04-03
Contact:
*(E-mail:guodalong@haust.edu.cn)
摘要:
DNA甲基化和mRNA可变剪接在果实发育过程中均发挥重要作用,但两者间的联系和互作关系尚不清楚。基于5-氮杂胞苷(5-azaC,DNA甲基转移酶抑制剂)处理可以使‘巨峰’葡萄成熟期提前,对5-azaC处理后的‘巨峰’RNA-seq测序,分析果实不同发育阶段发生的可变剪接事件。结果表明,3′端可变剪切位点(A3)类型在处理和对照中均最多,外显子互斥(MX)类型最少。可变剪接在不同发育阶段存在特异调节,发育前期可变剪接的调控更为频繁;鉴定到9 683个发育过程中保守的可变剪接事件。在处理与对照间有671个可变剪接事件存在明显的剪接变化,功能注释显示其中有14个基因与甲基化修饰相关,表明可变剪接与甲基化修饰协同调控葡萄果实成熟过程。
中图分类号:
马帅辉, 何光琪, 程一哲, 郭大龙. 5-azaC对‘巨峰’葡萄果实发育阶段mRNA可变剪接的影响[J]. 园艺学报, 2023, 50(3): 523-533.
MA Shuaihui, HE Guangqi, CHENG Yizhe, GUO Dalong. Analysis of Alternative Splicing at Different Developmental Stages of Kyoho Grapes with 5-azaC Treatment[J]. Acta Horticulturae Sinica, 2023, 50(3): 523-533.
处理 Treatment | 花后天数 Days post-anthesis | 原始序列 Raw data | 高质量序列 Clean data | 唯一比对率/% Unique mapping rate |
---|---|---|---|---|
5-azaC | 25 | 46 079 024 | 44 673 747 | 96.81 |
35 | 47 832 989 | 46 379 318 | 96.78 | |
45 | 48 174 649 | 46 431 546 | 96.76 | |
55 | 46 588 342 | 45 124 854 | 96.71 | |
65 | 46 919 474 | 45 539 185 | 96.25 | |
H2O(对照Control) | 25 | 47 422 767 | 45 914 784 | 96.89 |
35 | 48 921 036 | 47 464 829 | 96.81 | |
45 | 43 858 148 | 42 261 038 | 95.99 | |
55 | 47 506 354 | 45 916 451 | 96.42 | |
65 | 48 515 002 | 46 692 047 | 95.91 |
表1 果实样本采集及RNA-seq数据比对信息
Table 1 Fruit sample collection and RNA-seq data mapping information
处理 Treatment | 花后天数 Days post-anthesis | 原始序列 Raw data | 高质量序列 Clean data | 唯一比对率/% Unique mapping rate |
---|---|---|---|---|
5-azaC | 25 | 46 079 024 | 44 673 747 | 96.81 |
35 | 47 832 989 | 46 379 318 | 96.78 | |
45 | 48 174 649 | 46 431 546 | 96.76 | |
55 | 46 588 342 | 45 124 854 | 96.71 | |
65 | 46 919 474 | 45 539 185 | 96.25 | |
H2O(对照Control) | 25 | 47 422 767 | 45 914 784 | 96.89 |
35 | 48 921 036 | 47 464 829 | 96.81 | |
45 | 43 858 148 | 42 261 038 | 95.99 | |
55 | 47 506 354 | 45 916 451 | 96.42 | |
65 | 48 515 002 | 46 692 047 | 95.91 |
图1 ‘巨峰’葡萄可变剪接事件的鉴定 A:7类型可变剪接占比;B:已知和新发现的可变剪接事件占总体比例;C:共有和特有可变剪接占有效可变剪接事件比例;D:处理和对照有效可变剪接事件各类型比例;E:处理和对照中特有可变剪接事件各类型数量;F:RI和SE两种类型事件在总体和特有事件中的比例变化。
Fig. 1 Identification of alternative splicing(AS)events in Kyoho A:Overall proportion ofseven types of AS;B:Overall proportion of known and novel AS events;C:Proportion of common and unique AS to effective AS events;D:Proportion of each type of effective AS events in the treatment and control groups;E:Number of each type of unique AS events in the treatment and control groups;F:Change in proportion of both RI and SE types of events in the overall and unique AS events.
图3 ‘巨峰’葡萄5-azaC处理和对照可变剪接事件数量对比 A:可变剪接各类型数;B和C:5个采样时间可变剪接事件;D:保守可变剪接事件。
Fig. 3 Comparison of the number of AS events in Kyoho 5-azaC treatment and control A:Number of Number of AS types;B and C:Comparison of AS events at five sampling points in the control group(C1-C5)and treatment group(A1-A5);D:Comparison of conservative AS events in the treatment and control groups.
图4 ‘巨峰’葡萄5-azaC处理与对照差异可变剪接事件数量统计 C1 ~ C5和A1 ~ A5分别为对照和处理花后25、35、45、55和65 d的样本。
Fig. 4 Statistics on the number of DAS events between the 5-azaC treatment and control in kyoho C1-C5 and A1-A5 are samples from 25,35,45,55 and 65 d after flowering for control and treatment,respectively.
图5 Vitvi11g01240基因位点测序结果可视化 红色箭头表示可变剪接位置,“A3”字样表示可变剪接类型,下方数字表示所在基因组位置,左上数字表示reads取值范围。
Fig. 5 Visualization of sequencing results for the Vitvi11g01240 locus Red arrows indicate alternative splicing positions.“A3”character indicate the alternative splicing type,the lower numbers indicated the location site in the genome,the upper numbers showed the value range of the reads.
差异组 Difference group | 可变剪接事件ID AS_events ID | 参考基因组ID Reference genome ID | Swissprot注释 Swissprot annotation | 剪接率变化 ΔPSI | P |
---|---|---|---|---|---|
A1 vs. C1 | MSTRG.15527;A3:chr11:18854416-18855518:18854416-18855521:+ | Vitvi11g01240 | Q803K4|N-lysine methyltransferase setd6 | -0.385000 | 0.016983 |
MSTRG.24077;A3:chr18:4489688-4490608:4488547-4490608:- | Vitvi18g00414 | Q9C9Q8|Probable pectin methylransferase QUA2 | -0.954810 | 0.013986 | |
MSTRG.27205;A5:chr19:23341818-23342980:23341818-23342984:- | Vitvi19g01686 | O34614|Putative rRNA methylase YtqB | 0.238771 | 0.042957 | |
MSTRG.42;A3:chr00:3483728-3498435:3483728-3498440:+ | Vitvi07g02774 | O49354|Ubiquinone biosynthesis O-methyltransferase,mitochondrial | 0.397344 | 0.003996 | |
A2 vs. C2 | MSTRG.14725;SE:chr11:2089410-2089537:2089678-2089991:+ | Vitvi11g00218 | Q9C5D7|Probable caffeoyl-CoA O-methyltransferase At4g26220 | -0.218300 | 0.011988 |
MSTRG.22755;A3:chr17:1079931-1080008:1079931-1080110:+ | Vitvi17g00106 | Q6NMK1|Glucuronoxylan 4-O-methyltransferase 1 | 0.436952 | 0.036963 | |
MSTRG.4536;AL:chr03:17733301-17735190:17735272:17733301-17736694:17736812:+ | Vitvi03g01141 | Q8VXV7|Lysine-specific histone demethylase 1 homolog 1 | 0.953023 | 0.003996 | |
MSTRG.6764;A5:chr05:9227636-9227771:9227636-9227788:- | Vitvi05g00821 | Q8W595|Histone-lysine N-methyltransferase SUVR4 | 0.340451 | 0.036963 | |
MSTRG.9695;A5:chr07:16439920-16440048:16439920-16440056:- | Vitvi07g01181 | P19672|Putative rRNA methyltransferase YqxC | -0.214630 | 0.032967 | |
A3 vs. C3 | MSTRG.3140;A3:chr02:6450274-6450465:6450274-6450502:+ | Vitvi02g01481 | Q8GT41|PLA1_PLAAC(Putative invertase inhibitor | -0.298220 | 0.047952 |
MSTRG.5600;RI:chr04:19046492:19046896-19046989:19047215:- | Vitvi04g01339 | Q9FYZ9|Benzoate carboxyl methyltransferase | -0.425830 | 0.018482 | |
A4 vs. C4 | MSTRG.4755;A5:chr04:1209673-1211033:1209641-1211033:+ | Vitvi04g00134 | Q96P11|Probable 28S rRNA(cytosine-C(5))- methyltransferase | 0.922624 | 0.044955 |
A5 vs. C5 | MSTRG.17335;A3:chr13:1446344-1446866:1446344-1446940:+ | Vitvi13g00159 | B6YUU9|tRNA(guanine(26)- N(2))-dimethyltransferase | 0.482021 | 0.040460 |
MSTRG.17774;A3:chr13:6735007-6735041:6734974-6735041:- | Vitvi13g00674 | F4JW79|Protein RNA-directed DNA methylation 3 | 0.638740 | 0.016983 |
表2 与甲基化相关的差异可变剪接事件
Table 2 DAS events associated with methylation
差异组 Difference group | 可变剪接事件ID AS_events ID | 参考基因组ID Reference genome ID | Swissprot注释 Swissprot annotation | 剪接率变化 ΔPSI | P |
---|---|---|---|---|---|
A1 vs. C1 | MSTRG.15527;A3:chr11:18854416-18855518:18854416-18855521:+ | Vitvi11g01240 | Q803K4|N-lysine methyltransferase setd6 | -0.385000 | 0.016983 |
MSTRG.24077;A3:chr18:4489688-4490608:4488547-4490608:- | Vitvi18g00414 | Q9C9Q8|Probable pectin methylransferase QUA2 | -0.954810 | 0.013986 | |
MSTRG.27205;A5:chr19:23341818-23342980:23341818-23342984:- | Vitvi19g01686 | O34614|Putative rRNA methylase YtqB | 0.238771 | 0.042957 | |
MSTRG.42;A3:chr00:3483728-3498435:3483728-3498440:+ | Vitvi07g02774 | O49354|Ubiquinone biosynthesis O-methyltransferase,mitochondrial | 0.397344 | 0.003996 | |
A2 vs. C2 | MSTRG.14725;SE:chr11:2089410-2089537:2089678-2089991:+ | Vitvi11g00218 | Q9C5D7|Probable caffeoyl-CoA O-methyltransferase At4g26220 | -0.218300 | 0.011988 |
MSTRG.22755;A3:chr17:1079931-1080008:1079931-1080110:+ | Vitvi17g00106 | Q6NMK1|Glucuronoxylan 4-O-methyltransferase 1 | 0.436952 | 0.036963 | |
MSTRG.4536;AL:chr03:17733301-17735190:17735272:17733301-17736694:17736812:+ | Vitvi03g01141 | Q8VXV7|Lysine-specific histone demethylase 1 homolog 1 | 0.953023 | 0.003996 | |
MSTRG.6764;A5:chr05:9227636-9227771:9227636-9227788:- | Vitvi05g00821 | Q8W595|Histone-lysine N-methyltransferase SUVR4 | 0.340451 | 0.036963 | |
MSTRG.9695;A5:chr07:16439920-16440048:16439920-16440056:- | Vitvi07g01181 | P19672|Putative rRNA methyltransferase YqxC | -0.214630 | 0.032967 | |
A3 vs. C3 | MSTRG.3140;A3:chr02:6450274-6450465:6450274-6450502:+ | Vitvi02g01481 | Q8GT41|PLA1_PLAAC(Putative invertase inhibitor | -0.298220 | 0.047952 |
MSTRG.5600;RI:chr04:19046492:19046896-19046989:19047215:- | Vitvi04g01339 | Q9FYZ9|Benzoate carboxyl methyltransferase | -0.425830 | 0.018482 | |
A4 vs. C4 | MSTRG.4755;A5:chr04:1209673-1211033:1209641-1211033:+ | Vitvi04g00134 | Q96P11|Probable 28S rRNA(cytosine-C(5))- methyltransferase | 0.922624 | 0.044955 |
A5 vs. C5 | MSTRG.17335;A3:chr13:1446344-1446866:1446344-1446940:+ | Vitvi13g00159 | B6YUU9|tRNA(guanine(26)- N(2))-dimethyltransferase | 0.482021 | 0.040460 |
MSTRG.17774;A3:chr13:6735007-6735041:6734974-6735041:- | Vitvi13g00674 | F4JW79|Protein RNA-directed DNA methylation 3 | 0.638740 | 0.016983 |
图6 可变剪接事件验证 浅绿色矩形为外显子区域,黑线表示内含子区域,“F”表示正向引物位置,“R”表示反向引物位置,“alternative1”和“alternative2”表示可变剪接事件的两种不同剪接形式。
Fig. 6 Alternative splicing events validation The light green rectangle represents the exon region,the black line represents the intron region,“F”represents the forward primer position,“R”represents the reverse primer position,and“alternative1”and“alternative2”represent two different splicing forms of the alternative splicing events.
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