Genome-wide identification and expression analysis of the <i>β</i>-amylase gene family in <i>Ipomoea batatas</i>

HUANG Xiaofang; BI Chuyun; HUANG Weiqun; LIU Jianghong; HU Yunzhuo; HUANG Bifang; LIN Shiqiang; CHEN Xuanyang

doi:10.7671/j.issn.1001-411X.202011031

Journal of South China Agricultural University > 2021 > 42(5): 50-59. > DOI: 10.7671/j.issn.1001-411X.202011031

HUANG Xiaofang, BI Chuyun, HUANG Weiqun, et al. Genome-wide identification and expression analysis of the β-amylase gene family in Ipomoea batatas[J]. Journal of South China Agricultural University, 2021, 42(5): 50-59. DOI: 10.7671/j.issn.1001-411X.202011031

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Genome-wide identification and expression analysis of the β-amylase gene family in Ipomoea batatas

HUANG Xiaofang^{1, 2,},
BI Chuyun^{1, 2},
HUANG Weiqun³,
LIU Jianghong¹,
HU Yunzhuo¹,
HUANG Bifang⁴,
LIN Shiqiang^{1, 4, 5, ,},
CHEN Xuanyang^{1, 2, 6, ,}

1.
Key Laboratory of Crop Biotechnology in Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2.
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
3.
Seed Centre of Fujian, Fuzhou 350003, China
4.
College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
5.
Fujian Engineering and Technology Research Center of Breeding and Utilization for Special Crop, Fuzhou 350002, China
6.
Key Laboratory of Genetics, Breeding and Multiple Application of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China

More Information

Received Date: November 24, 2020
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
To mine the sequence information of the β-amylase gene family of Ipomoea batatas genome, and analyze the structure and function of genes.

Method
Based on the whole genome sequence data of I. batatas cultivar ‘Taizhong 6’, the bioinformatic methods were applied to analyze the identified 12 members of the β-amylase gene family and conduct the domain conservation analysis, chromosomal localization, screening of potential duplication genes, conservative motif analysis, phylogenetic tree construction. The gene expression under low temperature stress was analyzed using the transcriptomics data.

Result
Twelve β-amylase genes were located on chromosomes No. 2, 4, 5, 6, 11, 12, 13 and 14 of I. batatas, and eight pairs showed potential duplication relationship. Multiple sequence alignment and functional domain search indicated that there were three highly conserved domains and 10 conservative motifs in the amino acid sequences of I. batatas β-amylase family. Phylogenetic trees of β-amylase proteins in I. batatas and other species showed that 62 β-amylase family members were divided into seven subgroups of S1−S7. The β-amylases of I. batatas were mainly distributed in the subgroups of S2, S4, S5, S6 and S7, most of which belonged to the same branches with Arabidopsis thaliana, Solanum tuberosum and S. lycopersicum. The results of transcriptomics data showed that six β-amylase genes expressed differentially during the low temperature storage period, of which two were up-regulated and four were down-regulated in ‘Xushu 15-1’, while only two genes were down-regulated in ‘Xushu 15-4’.

Conclusion
The β-amylases are a key class of starch hydrolyzing enzymes that play important roles in the degradation of starch into reducing sugars during the process of I. batatas growth, development and tuber storage stages. The sequences of the identified 12 sweet potato β-amylase genes provide data reference for further study on the biological functions of I. batatas β-amylase gene family.
- Ipomoea batatas,
- β-amylase,
- gene family,
- systematic evolution,
- differential expression analysis

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References (31)

References

[1]	张勇为, 张义正, 谭文芳, 等. 甘薯贮藏期间淀粉酶种类变化及其部分性质分析[J]. 四川大学学报(自然科学版), 2018, 55(1): 197-200.
[2]	TODA H, NITTA Y, ASANAMI S, et al. Sweet potato β-amylase: Primary structure and identification of the active-site glutamyl residue[J]. European Journal of Biochemistry, 1993, 216(1): 25-38. doi: 10.1111/j.1432-1033.1993.tb18112.x
[3]	孙俊良, 梁新红, 贾彦杰, 等. 植物β−淀粉酶研究进展[J]. 河南科技学院学报(自然科学版), 2011, 39(6): 1-4.
[4]	LI H S, ÔBA K. Major soluble proteins of sweet potato roots and changes in proteins after cutting, infection, or storage[J]. Agricultural and Biological Chemistry, 2014, 49(3): 737-744.
[5]	NAKAMURA K, OHTO M A, YOSHIDA N, et al. Sucrose-induced accumulation of beta-amylase occurs concomitant with the accumulation of starch and sporamin in leaf-petiole cuttings of sweet potato[J]. Plant Physiology, 1991, 96(3): 902-909. doi: 10.1104/pp.96.3.902
[6]	梁新红, 李英, 孙俊良, 等. β−淀粉酶酶解甘薯淀粉条件分析[J]. 食品工业科技, 2014, 35(7): 178-181.
[7]	陈显让, 李红兵, 康乐, 等. 甘薯块根膨大后期β−淀粉酶和淀粉含量相关性分析[J]. 食品工业科技, 2013, 34(19): 93-96.
[8]	CHEONG C G, EOM S H, CHANG C, et al. Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato[J]. Proteins, 1995, 21(2): 105-117. doi: 10.1002/prot.340210204
[9]	YANG J, MOEINZADEH M H, KUHL H, et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history[J]. Nature Plants, 2017, 3(9): 696-703. doi: 10.1038/s41477-017-0002-z
[10]	黄小芳, 毕楚韵, 石媛媛, 等. 甘薯基因组NBS-LRR类抗病家族基因挖掘与分析[J]. 作物学报, 2020, 46(8): 1195-1207.
[11]	ALTSCHUL S F, GISH W, MILLER W, et al. Basic local alignment search tool[J]. Journal of Molecular Biology, 1990, 215(3): 403-410. doi: 10.1016/S0022-2836(05)80360-2
[12]	LU S, WANG J, CHITSAZ F, et al. CDD/SPARCLE: The conserved domain database in 2020[J]. Nucleic Acids Research, 2020, 48(D1): D265-D268. doi: 10.1093/nar/gkz991
[13]	QUEVILLON E, SILVENTOINEN V, PILLAI S, et al. InterProScan: Protein domains identifier[J]. Nucleic Acids Research, 2005, 33: W116-W120. doi: 10.1093/nar/gki442
[14]	SIEVERS F, HIGGINS D G. Clustal Omega for making accurate alignments of many protein sequences[J]. Protein Science, 2018, 27(1): 135-145. doi: 10.1002/pro.3290
[15]	KRZYWINSKI M, SCHEIN J, BIROL I, et al. Circos: An information aesthetic for comparative genomics[J]. Genome Research, 2009, 19(9): 1639-1645. doi: 10.1101/gr.092759.109
[16]	GU Z, CAVALCANTI A, CHEN F C, et al. Extent of gene duplication in the genomes of drosophila, nematode, and yeast[J]. Molecular Biology and Evolution, 2002, 19(3): 256-262. doi: 10.1093/oxfordjournals.molbev.a004079
[17]	BAILEY T L, BODEN M, BUSKE F A, et al. MEME SUITE: Tools for motif discovery and searching[J]. Nucleic Acids Research, 2009, 37: W202-W208. doi: 10.1093/nar/gkp335
[18]	KUMAR S, STECHER G, LI M, et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6): 1547-1549. doi: 10.1093/molbev/msy096
[19]	JI C Y, KIM H S, LEE C J, et al. Comparative transcriptome profiling of tuberous roots of two sweetpotato lines with contrasting low temperature tolerance during storage[J]. Gene, 2020: 727. doi: 10.1016/j.gene.2019.144244.
[20]	KIM D, LANGMEAD B, SALZBERG S L. HISAT: A fast spliced aligner with low memory requirements[J]. Nature Methods, 2015, 12(4): 357-360. doi: 10.1038/nmeth.3317
[21]	LOVE M I, HUBER W, ANDERS S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biology, 2014, 15(12). doi: 10.1186/s13059-014-0550-8.
[22]	TOTSUKA A, NONG V H, KADOKAWA H, et al. Residues essential for catalytic activity of soybean beta-amylase[J]. European Journal of Biochemistry, 1994, 221(2): 649-654.
[23]	WU S, LAU K H, CAO Q, et al. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement[J]. Nature Communications, 2018: 9. doi: 10.1038/s41467-018-06983-8.
[24]	THALMANN M, COIRO M, MEIER T, et al. The evolution of functional complexity within the β-amylase gene family in land plants[J]. BMC Evolutionary Biology, 2019: 19. doi: 10.1186/s12862-019-1395-2.
[25]	KANG Y N, ADACHI M, UTSUMI S, et al. The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase[J]. Journal of Molecular Biology, 2004, 339(5): 1129-1140. doi: 10.1016/j.jmb.2004.04.029
[26]	CHEN Y, CRIPPEN G M. An iterative refinement algorithm for consistency based multiple structural alignment methods[J]. Bioinformatics, 2006, 22(17): 2087-2093. doi: 10.1093/bioinformatics/btl351
[27]	VALERIO C, COSTA A, MARRI L, et al. Thioredoxin-regulated beta-amylase (BAM1) triggers diurnal starch degradation in guard cells, and in mesophyll cells under osmotic stress[J]. Journal of Experimental Botany, 2011, 62(2): 545-555. doi: 10.1093/jxb/erq288
[28]	杨泽峰, 徐暑晖, 王一凡, 等. 禾本科植物β−淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析[J]. 科技导报, 2014, 32(31): 29-36. doi: 10.3981/j.issn.1000-7857.2014.31.002
[29]	HOU J, ZHANG H, LIU J, et al. Amylases StAmy23, StBAM1 and StBAM9 regulate cold-induced sweetening of potato tubers in distinct ways[J]. Journal of Experimental Botany, 2017, 68(9): 2317-2331. doi: 10.1093/jxb/erx076
[30]	HATTORI T, FUKUMOTO H, NAKAGAWA S, et al. Sucrose-induced expression of genes coding for the tuberous root storage protein, sporamin, of sweet potato in leaves and petioles[J]. Plant and Cell Physiology, 1991, 32(1): 79-86.
[31]	唐君, 周志林, 林冬兰, 等. 甘薯贮藏过程淀粉酶活性变化及对薯块芽萌发的影响[J]. 福建农业学报, 2010, 25(6): 699-702. doi: 10.3969/j.issn.1008-0384.2010.06.008

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