马铃薯miR319基因家族靶基因预测及其功能分析

doi:10.16420/j.issn.0513-353x.2021-1280

摘要/Abstract

摘要：

通过生物信息分析发现，马铃薯miR319基因家族（Stu-miR319）共有3个前体基因，可生成5种成熟序列。序列比对发现，miR319成熟体序列在不同物种间具有高度的保守性，保守位点的分布差异较大。通过构建miR319前体基因的系统演化树发现，Stu-miR319的3个前体基因分属不同分支，且不同物种间的演化关系存在差异。组织特异性表达分析结果表明，Stu-miR319的5种成熟体在叶片中均有高表达。通过构建Stu-miR319前体基因过量表达转基因植株以及转录组测序分析发现，Stu-miR319-5p、Stu-miR319-3p、Stu-miR319a-5p和Stu-miR319b各有4个候选靶基因，Stu-miR319a-3p有2个候选靶基因。通过透射电镜分析发现，在Stu-miR319过量表达的植株中，导管细胞的细胞壁均有降解趋势，说明Stu-miR319基因家族对调控导管细胞细胞壁的完整性具有重要作用。

关键词: 马铃薯, miR319, 靶基因, 细胞壁

Abstract:

The Stu-miR319 sequences were analyzed to illustrate the function of miR319 gene family in potato. The results showed that there were three Stu-miR319 precursor genes generating five mature sequences. Sequence alignment showed that miR319 mature sequences were highly conserved among different species，while the conservative location distributions are quite different. Phylogenetic analysis revealed that these three Stu-miR319 precursor genes belonged to different clades，which had different evolutionary relationships. Tissue specific expression analysis showed that five mature Stu-miR319 were highly expressed in leaves. Three Stu-miR319 precursor genes overexpressing transgenic lines were generated，and the candidate targets of each Stu-miR319 mature sequences were analyzed. The results showed that each of Stu-miR319-5p，Stu-miR319-3p，Stu-miR319A-5p and Stu-miR319b have four candidate targets，while Stu-miR319a-3p has only two. Transmission electron microscopy analysis showed that the cell wall of leaf vessel elements in lines with Stu-miR319 overexpressing was severely degraded. The results indicate that the Stu-miR319 gene family plays an important role in regulating the cell wall integrity of leaf vessel elements.

Key words: potato, miR319, target gene, cell wall

中图分类号:

S532

尹健, 朱曦鉴, 吴瑶瑶, 李灿辉, 张金喆. 马铃薯miR319基因家族靶基因预测及其功能分析[J]. 园艺学报, 2023, 50(3): 583-595.

YIN Jian, ZHU Xijian, WU Yaoyao, LI Canhui, ZHANG Jinzhe. Targets Prediction and Function Analysis of Potato miR319 Gene Family[J]. Acta Horticulturae Sinica, 2023, 50(3): 583-595.

图/表 11

参考文献 37

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用途 Usage	引物名称 Primer name	序列（5′-3′） Primer sequence		退火温度/℃ T_m	产物大小/bp Product size
qRT-PCR 内参Reference	miR319-5p	F：AGGAAACTGTTTAGTCCAACC		53	80
	miR319-3p	F：TTGGACTGAAGGGTTCCC		55	80
	miR319a-5p	F：AGAGCTTTCTTCGGTCCA		54	80
	miR319a-3p	F：CGTTGGACTGAAGGGAGCTC		58	81
	18S rRNA	F：TTAGAGGAAGGAGAAGTCGTAACAA		56	270
	反向引物 Reverse primer	参照试剂盒According to the kits
克隆	miR319	F：AGGAAACTGTTTAGTCCAACCC	R：GAAGGGAACCCTTCAGTCCA	56	177
Cloning	miR319a	F：AGAGCTTTCTTCGGTCCA	R：AGGGAGCTCCCTTCAGTC	56	172
	miR319b	F：GAGCTCCTTTCAGGCCAA	R：AGGAGCTCCCTTCAGTCCA	56	173
载体构建 Vector	miR319-infusion	F：GGGGACTCTAGAGGATCCCCGGGAG GAAACTGTTTAGTCCAACCC R：GAGCTGGTCACCAATTCACACGTGGAAGGGAACCCTTCAGTCCA		60	224
construction	miR319a-infusion	F：GGGGACTCTAGAGGATCCCCGGGA GAGCTTTCTTCGGTCCA R：GAGCTGGTCACCAATTCACACGTGAGGGAGCTCCCTTCAGTC		60	219
	miR319b-infusion	F：GGGGACTCTAGAGGATCCCCGGGAGCTCCTTTCAGGCCAA R：GAGCTGGTCACCAATTCACACGTGAGGAGCTCCCTTCAGTCCA		60	220
内参Reference	St-Qp-ACT	F：GGGATGGAGAAGTTTGGTGGTGG	R：CTTCGACCAAGGGATGGTGTAGC	61	166
qRT-PCR	07G023850.1	F：GTCTACAGGGCGGAAAGACC	R：GCTCATCAATGGCGGGTTTC	58	185
	03G015060.1	F：GGAGCCAAGCACCCTTTAGT	R：TGAGCCTCTCTTGGCTTGTG	59	153
	03G022350.1	F：CAAGATTCGAACCGTGTGGC	R：ATGTCCACCCGGTACCTTCA	59	150
	07G025630.1	F：GTCTCATTGATCCAGCGGGT	R：GCTTCAGCGGGGTCAGTAAT	59	154
	04G012100	F：TGCTGATCCCAACGTACGAA	R：ATCAATGTTCGCGCTCCCTT	59	196
	02G018740	F：GGGGATGCTGGATTTATGCCT	R：TGGATCAAGCATTTGCAGCAG	59	171
	08G019310	F：CTTGACAAGGCGGAGTTTGC	R：TCACCACCTCTCTTTGGCAC	58	179
	10G001090	F：CACACAAGGTGTTGTTTGGCA	R：CCTTTCGGCCTTAACCAAGC	58	200
	11G005050	F：TAGCCTCTCATTTGCAAGGGG	R：ACAGCTGAGCTTTCCATGTC	59	190
	03G033500	F：GAGGCCAGAGTCGGAAACAA	R：GGATCTGAACTGCCTTCGGT	59	173
	08G015120	F：AGGTGTCTGGCTCAGGATTC	R：CCATCGTCTTCATCGATGCCT	60	187
	01G032600	F：TGCACTTGCGTATGAAGGCT	R：GTCCACACGCATAGCAGGTA	60	187
	06G017770	F：CCTTCGAAATTCCTCCGGCT	R：CAGCTGCAATCATCGCGAAA	60	186
	05G018750	F：TGGTGGCTCAAAGTGTGTTCT	R：GCACCAAGGGCATTGATTGG	59	172
	03G029210	F：CTCTGCCAAGAGTGGAGCAA	R：GTCTTGCAAGCCCGATACCA	60	165
	01G025250	F：TGCAACGATGATTGCTGTGC	R：CCAACAAGGCCGCACATTAG	59	150
	12G005850	F：ACAGCTGCCTAAGTTGGCTT	R：AGGCATCCAGCTTTCTTGCT	59	194
	04G019680	F：CTATGGTCAATGGAGCGCGA	R：TTCAACAACTGCGCAACCTG	59	181
	08G030230	F：GTGCCAATCTGTGCATCGAC	R：AATGCGAGGGTGCCATAGAC	59	170
	08G000520	F：TGGTGACTGGGACAACACAT	R：TGGTCCAGAGTCCTCGAGTT	59	188
	08G015810	F：TGTCCCGTGGAGAGGTAGAG	R：ATCACCCGAAACACGCTTCA	59	173
	03G015040	F：TTCTATGTGGACGGAACGCC	R：ACTAAAGGGTGCTTGGCTCC	59	168

用途 Usage	引物名称 Primer name	序列（5′-3′） Primer sequence		退火温度/℃ T_m	产物大小/bp Product size
qRT-PCR 内参Reference	miR319-5p	F：AGGAAACTGTTTAGTCCAACC		53	80
	miR319-3p	F：TTGGACTGAAGGGTTCCC		55	80
	miR319a-5p	F：AGAGCTTTCTTCGGTCCA		54	80
	miR319a-3p	F：CGTTGGACTGAAGGGAGCTC		58	81
	18S rRNA	F：TTAGAGGAAGGAGAAGTCGTAACAA		56	270
	反向引物 Reverse primer	参照试剂盒According to the kits
克隆	miR319	F：AGGAAACTGTTTAGTCCAACCC	R：GAAGGGAACCCTTCAGTCCA	56	177
Cloning	miR319a	F：AGAGCTTTCTTCGGTCCA	R：AGGGAGCTCCCTTCAGTC	56	172
	miR319b	F：GAGCTCCTTTCAGGCCAA	R：AGGAGCTCCCTTCAGTCCA	56	173
载体构建 Vector	miR319-infusion	F：GGGGACTCTAGAGGATCCCCGGGAG GAAACTGTTTAGTCCAACCC R：GAGCTGGTCACCAATTCACACGTGGAAGGGAACCCTTCAGTCCA		60	224
construction	miR319a-infusion	F：GGGGACTCTAGAGGATCCCCGGGA GAGCTTTCTTCGGTCCA R：GAGCTGGTCACCAATTCACACGTGAGGGAGCTCCCTTCAGTC		60	219
	miR319b-infusion	F：GGGGACTCTAGAGGATCCCCGGGAGCTCCTTTCAGGCCAA R：GAGCTGGTCACCAATTCACACGTGAGGAGCTCCCTTCAGTCCA		60	220
内参Reference	St-Qp-ACT	F：GGGATGGAGAAGTTTGGTGGTGG	R：CTTCGACCAAGGGATGGTGTAGC	61	166
qRT-PCR	07G023850.1	F：GTCTACAGGGCGGAAAGACC	R：GCTCATCAATGGCGGGTTTC	58	185
	03G015060.1	F：GGAGCCAAGCACCCTTTAGT	R：TGAGCCTCTCTTGGCTTGTG	59	153
	03G022350.1	F：CAAGATTCGAACCGTGTGGC	R：ATGTCCACCCGGTACCTTCA	59	150
	07G025630.1	F：GTCTCATTGATCCAGCGGGT	R：GCTTCAGCGGGGTCAGTAAT	59	154
	04G012100	F：TGCTGATCCCAACGTACGAA	R：ATCAATGTTCGCGCTCCCTT	59	196
	02G018740	F：GGGGATGCTGGATTTATGCCT	R：TGGATCAAGCATTTGCAGCAG	59	171
	08G019310	F：CTTGACAAGGCGGAGTTTGC	R：TCACCACCTCTCTTTGGCAC	58	179
	10G001090	F：CACACAAGGTGTTGTTTGGCA	R：CCTTTCGGCCTTAACCAAGC	58	200
	11G005050	F：TAGCCTCTCATTTGCAAGGGG	R：ACAGCTGAGCTTTCCATGTC	59	190
	03G033500	F：GAGGCCAGAGTCGGAAACAA	R：GGATCTGAACTGCCTTCGGT	59	173
	08G015120	F：AGGTGTCTGGCTCAGGATTC	R：CCATCGTCTTCATCGATGCCT	60	187
	01G032600	F：TGCACTTGCGTATGAAGGCT	R：GTCCACACGCATAGCAGGTA	60	187
	06G017770	F：CCTTCGAAATTCCTCCGGCT	R：CAGCTGCAATCATCGCGAAA	60	186
	05G018750	F：TGGTGGCTCAAAGTGTGTTCT	R：GCACCAAGGGCATTGATTGG	59	172
	03G029210	F：CTCTGCCAAGAGTGGAGCAA	R：GTCTTGCAAGCCCGATACCA	60	165
	01G025250	F：TGCAACGATGATTGCTGTGC	R：CCAACAAGGCCGCACATTAG	59	150
	12G005850	F：ACAGCTGCCTAAGTTGGCTT	R：AGGCATCCAGCTTTCTTGCT	59	194
	04G019680	F：CTATGGTCAATGGAGCGCGA	R：TTCAACAACTGCGCAACCTG	59	181
	08G030230	F：GTGCCAATCTGTGCATCGAC	R：AATGCGAGGGTGCCATAGAC	59	170
	08G000520	F：TGGTGACTGGGACAACACAT	R：TGGTCCAGAGTCCTCGAGTT	59	188
	08G015810	F：TGTCCCGTGGAGAGGTAGAG	R：ATCACCCGAAACACGCTTCA	59	173
	03G015040	F：TTCTATGTGGACGGAACGCC	R：ACTAAAGGGTGCTTGGCTCC	59	168

miRNA名称 miRNA name	靶基因 Target gene	功能注释 Function annotation
miR319-5p	Soltu.DM.04G019680	铵转运体1；2 Ammonium transporter 1；2
	Soltu.DM.08G030230	UDP-糖基转移酶家族蛋白 UDP-Glycosyltransferase superfamily protein
	Soltu.DM.08G000520	硝酸盐转运体1.1 Nitrate transporter 1.1
	Soltu.DM.08G015810	双BRCT结构域蛋白 Twin BRCT domain containing protein
miR319-3p	Soltu.DM.05G018750	葡萄糖-6-磷酸盐/磷酸盐转运体 Glucose-6-phosphate/phosphate translocator
	Soltu.DM.03G029210	RPA70-kDa亚单位B RPA70-kDa subunit B
	Soltu.DM.01G025250	HCO3转运体家族 HCO3-transporter family
	Soltu.DM.12G005850	UDP-葡糖基转移酶73B2 UDP-glucosyltransferase 73B2
miR319a-5p	Soltu.DM.08G019310	含有DUF_B2219结构域蛋白 Protein of unknown function（DUF_B2219）domain containing protein
	Soltu.DM.10G001090	Nudix水解酶同源物 Nudix hydrolase homolog
	Soltu.DM.11G005050	磷酸化酶家族蛋白 Phosphorylase superfamily protein
	Soltu.DM.03G033500	保守的假定蛋白 Conserved hypothetical protein
miR319a-3p	Soltu.DM.04G012100	含BTB/POZ结构域蛋白 BTB/POZ domain-containing protein
miR319a-3p	Soltu.DM.02G018740	ARM重复家族蛋白 ARM repeat superfamily protein
miR319b	Soltu.DM.08G015120	类胡萝卜素裂解双加氧酶 Carotenoid cleavage dioxygenase
	Soltu.DM.01G032600	含SPX（SYG1/Pho81/XPR1）结构域家族蛋白 Major Facilitator Superfamily with SPX（SYG1/Pho81/XPR1）domain-containing protein
	Soltu.DM.04G012100	含BTB/POZ结构域蛋白 BTB/POZ domain-containing protein
	Soltu.DM.06G017770	硝酸盐转运体1.1 Nitrate transporter 1.1

miRNA名称 miRNA name	靶基因 Target gene	功能注释 Function annotation
miR319-5p	Soltu.DM.04G019680	铵转运体1；2 Ammonium transporter 1；2
	Soltu.DM.08G030230	UDP-糖基转移酶家族蛋白 UDP-Glycosyltransferase superfamily protein
	Soltu.DM.08G000520	硝酸盐转运体1.1 Nitrate transporter 1.1
	Soltu.DM.08G015810	双BRCT结构域蛋白 Twin BRCT domain containing protein
miR319-3p	Soltu.DM.05G018750	葡萄糖-6-磷酸盐/磷酸盐转运体 Glucose-6-phosphate/phosphate translocator
	Soltu.DM.03G029210	RPA70-kDa亚单位B RPA70-kDa subunit B
	Soltu.DM.01G025250	HCO3转运体家族 HCO3-transporter family
	Soltu.DM.12G005850	UDP-葡糖基转移酶73B2 UDP-glucosyltransferase 73B2
miR319a-5p	Soltu.DM.08G019310	含有DUF_B2219结构域蛋白 Protein of unknown function（DUF_B2219）domain containing protein
	Soltu.DM.10G001090	Nudix水解酶同源物 Nudix hydrolase homolog
	Soltu.DM.11G005050	磷酸化酶家族蛋白 Phosphorylase superfamily protein
	Soltu.DM.03G033500	保守的假定蛋白 Conserved hypothetical protein
miR319a-3p	Soltu.DM.04G012100	含BTB/POZ结构域蛋白 BTB/POZ domain-containing protein
miR319a-3p	Soltu.DM.02G018740	ARM重复家族蛋白 ARM repeat superfamily protein
miR319b	Soltu.DM.08G015120	类胡萝卜素裂解双加氧酶 Carotenoid cleavage dioxygenase
	Soltu.DM.01G032600	含SPX（SYG1/Pho81/XPR1）结构域家族蛋白 Major Facilitator Superfamily with SPX（SYG1/Pho81/XPR1）domain-containing protein
	Soltu.DM.04G012100	含BTB/POZ结构域蛋白 BTB/POZ domain-containing protein
	Soltu.DM.06G017770	硝酸盐转运体1.1 Nitrate transporter 1.1