Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing

doi:10.3969/j.issn.1004-1524.2021.11.09

Acta Agriculturae Zhejiangensis ›› 2021, Vol. 33 ›› Issue (11): 2068-2074.DOI: 10.3969/j.issn.1004-1524.2021.11.09

• Horticultural Science • Previous Articles Next Articles

Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing

TAO Peng(), YUE Zhichen, ZHAO Yanting, LEI Juanli, LI Biyuan^*()

Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2020-10-28 Online:2021-11-25 Published:2021-11-26
Contact: LI Biyuan

Abstract

Abstract:

To investigate the effect of variation of acceptor splicing site on splicing pattern and efficiency, the inbred line “He2” of Chinese cabbage was re-sequenced, and the result indicated that acceptor splicing site of the sixth intron (I6) of BrSPS1Fb-He2 was changed from AG to AC. Through analysis of BrSPS1Fb-He2 read data from transcriptome sequencing library of petals of the “He2” inbred line, it was found that alternative splicing occurred during pre-mRNA processing of BrSPS1Fb-He2. Three sites (A1, A2 and A3) of BrSPS1Fb-He2 could be selected as splicing acceptor during pre-mRNA splicing, resulting correspondingly in the three spliced isoforms (S1, S2 and S3), or the entire I6 was retained to form S4 spliced isoform. Partial I6 was retained in mature mRNA of S1 and S2, the whole I6 in S4, partial E7 was deleted in S3. This study indicated that single nucleotide polymorphisms (SNP) variation of acceptor splicing site had a significant impact on post transcriptional splicing of BrSPS1Fb.

Key words: Chinese cabbage, single nucleotide polymorphisms (SNP), acceptor splicing site, SPS1F, alternative splicing

CLC Number:

S634.1

TAO Peng, YUE Zhichen, ZHAO Yanting, LEI Juanli, LI Biyuan. Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing[J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2068-2074.

Figures/Tables 5

Table 1 Retrieval sequences

名称 Name	检索对象 Retrieval object	序列(5'-3') Sequence (5'-3')
PA	BrSPS1Fa	CGAGATCCACCAATATGGGCTGAG
PB	BrSPS1Fb	CGGGATCCACCAATATGGGCTGAG
PA1	BrSPS1Fa-S1	CGAGATCCACCAATATGGGCTGAGCTGT
PA2	BrSPS1Fa-S2	CGAGATCCACCAATATGGGCTGAGGTGA
PA3	BrSPS1Fa-S3	CGAGATCCACCAATATGGGCTGAGCCTA
PA4	BrSPS1Fa-S4	CGAGATCCACCAATATGGGCTGAGGTTC
PA5	BrSPS1Fa-S5	CGAGATCCACCAATATGGGCTGAGATAA
PB1	BrSPS1Fb-S1	CGGGATCCACCAATATGGGCTGAGAGCT
PB2	BrSPS1Fb-S2	CGGGATCCACCAATATGGGCTGAGGTGA
PB3	BrSPS1Fb-S3	CGGGATCCACCAATATGGGCTGAGCCTA
PB4	BrSPS1Fb-S4	CGGGATCCACCAATATGGGCTGAGGTTC
PB5	BrSPS1Fb-S5	CGGGATCCACCAATATGGGCTGAGATAA

Fig.1 Intron-exon structure of BrSPS1Fb-Chiifu401 of Chinese cabbage and SNP variation of acceptor splicing site of BrSPS1Fb in the inbred line He2 of Chinese cabbage

Fig.2 Splicing isoforms and location of splicing sites of BrSPS1Fb-He2 A, Four splicing isoforms of BrSPS1Fb-He2 of Chinese cabbage He2 and their corresponding donor splicing sites and acceptor splicing sites. B, Location of donor splicing sites and acceptor splicing sites of the BrSPS1Fb-He2 gene. Black and gray background represented the sequence of exon and intron, respectively.

Fig.3 Proportion of splicing isoforms of BrSPS1Fa and BrSPS1Fb of Chinese cabbage

Fig.4 Alignment of amino acid sequences of protein products of BrSPS1Fb-He2 of Chinese cabbage and BrSPS1Fb-Chiifu401 protein

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Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing

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