Identification and Expression Analysis of Members of the SWEET Gene Family in Chinese Chestnut

doi:10.13560/j.cnki.biotech.bull.1985.2024-0700

Abstract

Abstract:

Objective The SWEET gene family is closely related to the starch content and sugar content in the fruit. Focusing on the expression pattern of chestnut SWEET gene family during chestnut fruit ripening may lay the foundation for subsequent studies of the SWEET gene family function during fruit ripening in Chinese chestnut. Method Bioinformatics techniques was applied to identify the SWEET gene family of seven Fagaceae species. Phylogenetic tree was constructed on them, homology analysis of each member was performed, and gene duplication type analysis was performed, etc. The protein physicochemical properties, gene structure, selection pressure and protein structure of chestnut SWEET gene family were also analyzed. Transcriptome and RT-qPCR were used to analyze the expression patterns of chestnut SWEET gene family members during different fruit ripening period. Result A total of seven Fagaceae species contained the 129 members of SWEET gene family, and seven species had 16 SWEET gene family members before divergence. There were 19 chestnut SWEET gene families, which were unequally distributed across nine chromosomes and one contig segment. And their proteins had a relatively consistent Motif distribution and conserved domain distribution. The results of cis-element analysis showed that a large number of growth-related elements, hormone response elements and stress response elements were present on the promoter sequences of chestnut SWEET gene family. Transcriptome and RT-qPCR analyses revealed that nine members of the chestnut SWEET gene family were expressed during chestnut fruit ripening. Among them, CmSWEET1, CmSWEET3, CmSWEET4, CmSWEET16 and CmSWEET19 were downregulated with ripening, CmSWEET2 and CmSWEET9 were downregulated with ripening, and CmSWEET15 and CmSWEET17 were downregulated with ripening. Conclusion A total of 129 members of the Fagaceae species SWEET gene family are identified, including 19 members of the chestnut SWEET gene family.CmSWEET15 and CmSWEET17 expression pattern is similar to the change pattern of soluble sugars, which may regulate soluble sugar transport during chestnut fruit ripening. The expression patterns of CmSWEET1, CmSWEET2, CmSWEET3, CmSWEET4, CmSWEET9, CmSWEET16 and CmSWEET19 are completely consistent with or opposite to the pattern of starch changes, which may regulate starch accumulation during chestnut fruit ripening.

Key words: chestnut, Fagaceae, gene family, starch, soluble sugar, expression patterns, bioinformatics

YANG Yong, YUAN Guo-mei, KANG Xiao-xiao, LIU Ya-ming, WANG Dong-sheng, ZHANG Hai-e. Identification and Expression Analysis of Members of the SWEET Gene Family in Chinese Chestnut[J]. Biotechnology Bulletin, 2025, 41(2): 257-269.

Figures/Tables 14

References 35

1	Yamada K, Osakabe Y. Sugar compartmentation as an environmental stress adaptation strategy in plants [J]. Semin Cell Dev Biol, 2018, 83: 106-114.
2	Pommerrenig B, Ludewig F, Cvetkovic J, et al. In concert: orchestrated changes in carbohydrate homeostasis are critical for plant abiotic stress tolerance [J]. Plant Cell Physiol, 2018, 59(7): 1290-1299.
3	Chen LQ, Cheung LS, Feng L, et al. Transport of sugars [J]. Annu Rev Biochem, 2015, 84: 865-894.
4	Eom JS, Chen LQ, Sosso D, et al. SWEETs, transporters for intracellular and intercellular sugar translocation [J]. Curr Opin Plant Biol, 2015, 25: 53-62.
5	Xie HH, Wang D, Qin YQ, et al. Genome-wide identification and expression analysis of SWEET gene family in Litchi chinensis reveal the involvement of LcSWEET2a/3b in early seed development [J]. BMC Plant Biol, 2019, 19(1): 499.
6	Chen LQ, Qu XQ, Hou BH, et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport [J]. Science, 2012, 335(6065): 207-211.
7	Zhu JL, Zhou L, Li TF, et al. Genome-wide investigation and characterization of SWEET gene family with focus on their evolution and expression during hormone and abiotic stress response in maize [J]. Genes, 2022, 13(10): 1682.
8	Li M, Xie HJ, He MM, et al. Genome-wide identification and expression analysis of the StSWEET family genes in potato (Solanum tuberosum L.) [J]. Genes Genomics, 2020, 42(2): 135-153.
9	Hao L, Shi X, Qin SW, et al. Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale [J]. BMC Genomics, 2023, 24(1): 378.
10	Han XW, Han S, Zhu YX, et al. Genome-wide identification and expression analysis of the SWEET gene family in Capsicum annuum L [J]. Int J Mol Sci, 2023, 24(24): 17408.
11	Zhang XH, Wang S, Ren Y, et al. Identification, analysis and gene cloning of the SWEET gene family provide insights into sugar transport in pomegranate (Punica granatum) [J]. Int J Mol Sci, 2022, 23(5): 2471.
12	Li P, Wang LH, Liu HB, et al. Impaired SWEET-mediated sugar transportation impacts starch metabolism in developing rice seeds [J]. Crop J, 2022, 10(1): 98-108.
13	Radchuk V, Belew ZM, Gündel A, et al. SWEET11b transports both sugar and cytokinin in developing barley grains [J]. Plant Cell, 2023, 35(6): 2186-2207.
14	Zhang XS, Feng CY, Wang MN, et al. Plasma membrane-localized SlSWEET7a and SlSWEET14 regulate sugar transport and storage in tomato fruits [J]. Hortic Res, 2021, 8(1): 186.
15	Wang SD, Yokosho K, Guo RZ, et al. The soybean sugar transporter GmSWEET15 mediates sucrose export from endosperm to early embryo [J]. Plant Physiol, 2019, 180(4): 2133-2141.
16	Zhang SH, Wang H, Wang T, et al. Abscisic acid and regulation of the sugar transporter gene MdSWEET9b promote apple sugar accumulation [J]. Plant Physiol, 2023, 192(3): 2081-2101.
17	Massantini R, Moscetti R, Frangipane MT. Evaluating progress of chestnut quality: a review of recent developments [J]. Trends Food Sci Technol, 2021, 113: 245-254.
18	Warmund MR. Chinese chestnut (Castanea mollissima) as a niche crop in the central region of the United States [J]. HortScience, 2011, 46(3): 345-347.
19	Haytowitz D, Ahuja J, Wu X, et al. USDA National Nutrient Database for standard reference, legacy [EB/OL] . .
20	Huang RM, Peng F, Wang DS, et al. Transcriptome analysis of differential sugar accumulation in the developing embryo of contrasting two Castanea mollissima cultivars [J]. Front Plant Sci, 2023, 14: 1206585.
21	Rozewicki J, Li SL, Amada KM, et al. MAFFT-DASH: integrated protein sequence and structural alignment [J]. Nucleic Acids Res, 2019, 47(W1): W5-W10.
22	Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments [J]. PLoS One, 2010, 5(3): e9490.
23	Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics [J]. Genome Biol, 2019, 20(1): 238.
24	Xie JM, Chen YR, Cai GJ, et al. Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees [J]. Nucleic Acids Res, 2023, 51(W1): W587-W592.
25	Chen K, Durand D, Farach-Colton M. NOTUNG: a program for dating gene duplications and optimizing gene family trees [J]. J Comput Biol, 2000, 7(3/4): 429-447.
26	Chen CJ, Wu Y, Li JW, et al. TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining [J]. Mol Plant, 2023, 16(11): 1733-1742.
27	Wang YP, Tang HB, Debarry JD, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity [J]. Nucleic Acids Res, 2012, 40(7): e49.
28	Qiao X, Li QH, Yin H, et al. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants [J]. Genome Biol, 2019, 20(1): 38.
29	Abramson J, Adler J, Dunger J, et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3 [J]. Nature, 2024, 630(8016): 493-500.
30	Li SX, Shi ZG, Zhu QR, et al. Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia [J]. BMC Genomics, 2021, 22(1): 617.
31	Singh J, Das S, Jagadis Gupta K, et al. Physiological implications of SWEETs in plants and their potential applications in improving source-sink relationships for enhanced yield [J]. Plant Biotechnol J, 2023, 21(8): 1528-1541.
32	杜兵帅, 邹昕蕙, 王子豪, 等. 油茶SWEET基因家族的全基因组鉴定及表达分析 [J]. 生物技术通报, 2024, 40(5): 179-190.
	Du BS, Zou XH, Wang ZH, et al. Genome-wide identification and expression analysis of the SWEET gene family in Camellia oleifera [J]. Biotechnol Bull, 2024, 40(5): 179-190.
33	赵奇, 茹京娜, 李宜统, 等. 小麦Lhc基因家族鉴定与表达模式分析 [J]. 植物遗传资源学报, 2022, 23(6): 1766-1781.
	Zhao Q, Ru JN, Li YT, et al. Identification and expression pattern analysis of Lhc gene family members in wheat [J]. J Plant Genet Resour, 2022, 23(6): 1766-1781.
34	Qu JJ, Liu LL, Guo ZX, et al. The ubiquitous position effect, synergistic effect of recent generated tandem duplicated genes in grapevine, and their co-response and overactivity to biotic stress [J]. Fruit Res, 2023, 3(1).
35	Yu LY, Fei C, Wang DS, et al. Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima [J]. Front Genet, 2023, 14: 1193953.

基因Gene	上游引物Forward primer（5′-3′）	下游引物Reverse primer（5′-3′）
CmSWEET1	CTGCATGGTGTGGGCCTT	GATACCAGTGCCTGCCCC
CmSWEET2	GCGCTGTTTGTGTCACCC	AGCAGCTGAAGAAGGCGT
CmSWEET3	CAAAGGAAGCAGCCTCCCA	TGGGGCCAACTAGGGTGT
CmSWEET9	ATGCAGCTGGAGTCGCAG	CGGCAGCCCTGAGAACTG
CmSWEET14	GCTTTGCTGCTGCCGTTT	CAGGAAGTGCCGCACAGA
CmSWEET15	TCGCGTTTGTGCTCACCT	AAACGGCAGCAGCAAAGC
CmSWEET16	CAGCCGGGAGAGCTAGGA	AGCAGGGAGGTGCAAAGC
CmSWEET17	GCACCCGGGAGAGTTAGG	AGCAGGGAGGTGCAAAGC
CmSWEET19	CCTGGCAAAAGGCTCCCA	TGGCATGTACTCCACGCTC
CmActin	ATTCACGAGACCACCTACA	TGCCACAACCTTAATCTTCAT

基因Gene	上游引物Forward primer（5′-3′）	下游引物Reverse primer（5′-3′）
CmSWEET1	CTGCATGGTGTGGGCCTT	GATACCAGTGCCTGCCCC
CmSWEET2	GCGCTGTTTGTGTCACCC	AGCAGCTGAAGAAGGCGT
CmSWEET3	CAAAGGAAGCAGCCTCCCA	TGGGGCCAACTAGGGTGT
CmSWEET9	ATGCAGCTGGAGTCGCAG	CGGCAGCCCTGAGAACTG
CmSWEET14	GCTTTGCTGCTGCCGTTT	CAGGAAGTGCCGCACAGA
CmSWEET15	TCGCGTTTGTGCTCACCT	AAACGGCAGCAGCAAAGC
CmSWEET16	CAGCCGGGAGAGCTAGGA	AGCAGGGAGGTGCAAAGC
CmSWEET17	GCACCCGGGAGAGTTAGG	AGCAGGGAGGTGCAAAGC
CmSWEET19	CCTGGCAAAAGGCTCCCA	TGGCATGTACTCCACGCTC
CmActin	ATTCACGAGACCACCTACA	TGCCACAACCTTAATCTTCAT

物种 Species	全基因组复制 WGD	串联复制 TD	近端复制 PD	分散复制 DSD	转座子复制 TRD	总数 Total
欧洲山毛榉 Fagus sylvatica	1	0	2	1	2	6
槲树 Quercus dentata	3	2	1	1	3	10
红锥 Castanopsis hystrix	2	4	3	0	5	14
钩椎 Castanopsis tibetana	1	1	2	0	4	8
日本栗 Castanea crenata	1	1	2	3	4	11
美洲栗 Castanea dentata	3	5	1	0	2	11
板栗 Castanea mollissima	0	5	1	3	3	12

物种 Species	全基因组复制 WGD	串联复制 TD	近端复制 PD	分散复制 DSD	转座子复制 TRD	总数 Total
欧洲山毛榉 Fagus sylvatica	1	0	2	1	2	6
槲树 Quercus dentata	3	2	1	1	3	10
红锥 Castanopsis hystrix	2	4	3	0	5	14
钩椎 Castanopsis tibetana	1	1	2	0	4	8
日本栗 Castanea crenata	1	1	2	3	4	11
美洲栗 Castanea dentata	3	5	1	0	2	11
板栗 Castanea mollissima	0	5	1	3	3	12

复制类型Duplication type	基因对Gene pair		非同义替换率Ka	同义替换率Ks	非同义替换率/同义替换率Ka/Ks
TD	CmSWEET5	CmSWEET6	0.44	4.81	0.09
TD	CmSWEET18	CmSWEET19	0.34	1.77	0.19
TD	CmSWEET6	CmSWEET7	0.37	1.07	0.34
TD	CmSWEET14	CmSWEET15	0.04	0.12	0.37
TD	CmSWEET4	CmSWEET5	0.22	0.45	0.49
PD	CmSWEET16	CmSWEET17	0.02	0.06	0.28
DSD	CmSWEET8	CmSWEET11	0.64	1.69	0.38
DSD	CmSWEET13	CmSWEET11	0.57	3.47	0.16
DSD	CmSWEET11	CmSWEET3	0.45	2.14	0.21
TRD	CmSWEET9	CmSWEET2	0.23	0.98	0.23
TRD	CmSWEET1	CmSWEET12	0.42	3.06	0.14
TRD	CmSWEET10	CmSWEET17	0.33	1.73	0.19