Analysis of Alternative Splicing at Different Developmental Stages of Kyoho Grapes with 5-azaC Treatment

doi:10.16420/j.issn.0513-353x.2021-1196

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (3): 523-533.doi: 10.16420/j.issn.0513-353x.2021-1196

• Research Papers • Previous Articles Next Articles

Analysis of Alternative Splicing at Different Developmental Stages of Kyoho Grapes with 5-azaC Treatment

MA Shuaihui, HE Guangqi, CHENG Yizhe, GUO Dalong^*()

Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants，College of Horticulture and Plant Protection，Henan University of Science and Technology，Luoyang，Henan 471023，China

Received:2022-04-18 Revised:2022-10-03 Online:2023-03-25 Published:2023-04-03
Contact: *（E-mail：guodalong@haust.edu.cn）

Abstract

Abstract:

Both DNA methylation and alternative splicing play important roles in fruit development，but the links and the interactions between them during fruit development are unclear. In this study，alternative splicing events occurring at different developmental stages of 5-azacytidine（5-azaC，DNA methyltransferase inhibitors）treated and control berries of Kyoho from 25 to 65 days after flowering were analyzed based on RNA-seq data. The results showed that alternative 3′ splice site（A3）was the most frequent type and mutually exclusive exons（MX）was the least type revealed in both the treatment and control groups. There was stage-specific regulation of alternative splicing during grape berry development. The events of alternative splicing were more abundant at the early stages of berry development，and 9 683 was identified as the conserved events during berry development. There were 671 alternative splicing events which showed significant deviation between the treatments and controls，and functional annotation demonstrated that 14 of these genes were associated with methylation modifications. The significant differences in the extent of alternative splicing of these methylation-related genes in the treated and control groups suggest that alternative splicing and methylation modification synergistically regulate the grape berry ripening process.

Key words: grape, fruit development, DNA methyltransferase inhibitor, 5-azaC, alternative splicing, methylation

CLC Number:

S663.1

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.

Figures/Tables 8

References 30

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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

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

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

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

Analysis of Alternative Splicing at Different Developmental Stages of Kyoho Grapes with 5-azaC Treatment

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