梨Trihelix转录因子家族成员鉴定及表达分析

doi:10.16420/j.issn.0513-353x.2020-0421

摘要/Abstract

摘要：

Trihelix转录因子可以和光应答相关的GT元件结合,因此又称GT转录因子。本研究从梨基因组中鉴定出16个Trihelix家族基因,依次命名为PbGT1 ~ PbGT16,从同属于蔷薇科的草莓和桃基因组中分别鉴定出11和16个Trihelix家族基因。染色体定位与基因复制事件分析表明,梨、草莓和桃Trihelix家族成员分别分布在12、6和8条染色体上,且梨Trihelix家族存在片段复制事件。种间系统进化树分析表明,梨、草莓和桃Trihelix家族成员分为6个亚族,梨家族成员（PbGT）属于GT-2、Subfamily O和SIP1亚族。结合进化关系及qRT-PCR验证,筛选出PbGT15可能参与调控梨果实石细胞团木质化。

关键词: 梨, Trihelix转录因子, 比较基因组学, 表达分析, 木质化

Abstract:

Trihelix transcription factors（TFs）binded to light-responsive GT elements are called GT transcription factors. This study not only identified 16 members of the Trihelix family from the pear genome,named PbGT1-PbGT16 in turn,but also identified 11 and 16 members of the Trihelix family respectively from the genomes of strawberry and peach belonging to the Rosaceae family like pear. Chromosome localization showed that the Trihelix family members of pear,strawberry and peach were distributed on 12,6 and 8 chromosomes,respectively. Segmental duplication events were found in the Trihelix family of pear by gene duplication events analysis. The clustering result of interspecific phylogenetic tree showed that the Trihelix family members of pear,strawberry and peach were divided into six subfamilies and the Trihelix family members of pear（PbGTs） belong to the GT-2,Subfamily O and SIP1 subfamilies. Combined with evolutionary relationship and qRT-PCR verification,PbGT15 may be involved in regulating lignification of pear fruit stone cells.

Key words: pear, Trihelix transcription factors, comparative genomics, expression analysis, lignification

中图分类号:

S661.2

韩文龙, 朱振, 李君茹, 陈天哲, 李国辉, 苏雪强, 金青, 程曦, 蔡永萍. 梨Trihelix转录因子家族成员鉴定及表达分析[J]. 园艺学报, 2021, 48(3): 439-455.

HAN Wenlong, ZHU Zhen, LI Junru, CHEN Tianzhe, LI Guohui, SU Xueqiang, JIN Qin, CHENG Xi, CAI Yongping. Indentification and Expression Analysis of Trihelix Transcription Factor Family in Pear[J]. Acta Horticulturae Sinica, 2021, 48(3): 439-455.

图/表 12

参考文献 40

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基因名称 Gene name	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
PbGT1	AGTGAACTGACTCGAGCGATATTGA	ACTAGCATTCCCAACCCCGTTAACC
PbGT2	CACGGGTTGTTTTGTTTATTACCTT	TTGTTGCTGCTACGATGGTTACTAG
PbGT3	AGATGATGGAGCTGGAGAAACAGAG	AATGATCAAATAAAACCCATAAACA
PbGT4	GAATATGTTCATGGATGTTCAGGTG	TGCCTACATTGCAGTAATTCTTAAC
PbGT5	AAACCAGTGGTGATGGGACTAAGTG	TGCGACTTCATGATTTTCCATTTTT
PbGT6	AAAAGAGTAAAAGGAAGCAGATGGC	CAGATAGATACCGATATTACCCGCT
PbGT7	TTCGTATAGAGTGTTGGCGGATTCA	ATCATTCACTGAGATCGTCAACAGA
PbGT8	GTTGGAGTTGCAGAAGAAGCAGATT	AGATACCACACACCCTCACCTGCAT
PbGT9	TGCCTCTATGACGAGTCGGACCACA	GGAACGCGGTTCCCTCAACTCACAC
PbGT10	GCATCGGCAGCTTGTTACTTTCAGA	CACTGGTTTTGGCTTTCCGTGCTGA
PbGT11	CTCCTAATGGTGGGAATAATGCAAG	ATCATCACTGGTTTTGGCTTCCCTT
PbGT12	GAGGGACTTTCACCATTGTGTTCTA	TTCAAAAAATGCATCACCTGTCCAA
PbGT13	AGAATACAGGCCGTTCGTCTAACGG	ATTATCTCATTGAACCATGGCGAGG
PbGT14	AATAGGATGGAGGAAGCGGATAGCG	CACATAACTCACTGAACCATGGCGA
PbGT15	TAAGAATGATGCTAGTTATGTGGAG	GCCATTCTATCTCACTCGTATCATG
PbGT16	GAGGATTCAAAAACATGTCCATATT	TGATGACTCTTTCTAGTTGGTTACC
Tubulin	AGAACAAGAACTCGTCCTAC	GAACTGCTCGCTCACTCTCC

基因名称 Gene name	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
PbGT1	AGTGAACTGACTCGAGCGATATTGA	ACTAGCATTCCCAACCCCGTTAACC
PbGT2	CACGGGTTGTTTTGTTTATTACCTT	TTGTTGCTGCTACGATGGTTACTAG
PbGT3	AGATGATGGAGCTGGAGAAACAGAG	AATGATCAAATAAAACCCATAAACA
PbGT4	GAATATGTTCATGGATGTTCAGGTG	TGCCTACATTGCAGTAATTCTTAAC
PbGT5	AAACCAGTGGTGATGGGACTAAGTG	TGCGACTTCATGATTTTCCATTTTT
PbGT6	AAAAGAGTAAAAGGAAGCAGATGGC	CAGATAGATACCGATATTACCCGCT
PbGT7	TTCGTATAGAGTGTTGGCGGATTCA	ATCATTCACTGAGATCGTCAACAGA
PbGT8	GTTGGAGTTGCAGAAGAAGCAGATT	AGATACCACACACCCTCACCTGCAT
PbGT9	TGCCTCTATGACGAGTCGGACCACA	GGAACGCGGTTCCCTCAACTCACAC
PbGT10	GCATCGGCAGCTTGTTACTTTCAGA	CACTGGTTTTGGCTTTCCGTGCTGA
PbGT11	CTCCTAATGGTGGGAATAATGCAAG	ATCATCACTGGTTTTGGCTTCCCTT
PbGT12	GAGGGACTTTCACCATTGTGTTCTA	TTCAAAAAATGCATCACCTGTCCAA
PbGT13	AGAATACAGGCCGTTCGTCTAACGG	ATTATCTCATTGAACCATGGCGAGG
PbGT14	AATAGGATGGAGGAAGCGGATAGCG	CACATAACTCACTGAACCATGGCGA
PbGT15	TAAGAATGATGCTAGTTATGTGGAG	GCCATTCTATCTCACTCGTATCATG
PbGT16	GAGGATTCAAAAACATGTCCATATT	TGATGACTCTTTCTAGTTGGTTACC
Tubulin	AGAACAAGAACTCGTCCTAC	GAACTGCTCGCTCACTCTCC

物种 Species	基因编号 Gene ID	基因名称 Gene name	染色体 Chr	蛋白质Protein
物种 Species	基因编号 Gene ID	基因名称 Gene name	染色体 Chr	等电点 pI	长度/aa Length	分子质量/kD Molecular weight	亚细胞定位 Subcellular localization
梨	Pbr022283.1	PbGT1	Chr17	8.34	585	63.32	细胞核 Nuclear
Pear	Pbr027539.1	PbGT2	Chr9	9.61	350	38.01	细胞核 Nuclear
	Pbr009547.1	PbGT3	Chr1	9.27	247	27.90	细胞核 Nuclear
	Pbr010927.1	PbGT4	Chr7	9.20	241	27.34	细胞核 Nuclear
	Pbr016131.2	PbGT5	Chr10	5.50	448	49.17	细胞核 Nuclear
	Pbr034589.1	PbGT6	Chr5	4.70	398	45.36	细胞核 Nuclear
	Pbr027585.1	PbGT7	Chr2	4.79	363	42.82	细胞核 Nuclear
	Pbr015453.1	PbGT8	Chr15	4.90	360	42.54	细胞核 Nuclear
	Pbr036250.1	PbGT9	Chr16	5.95	426	48.87	细胞核 Nuclear
	Pbr016796.1	PbGT10	Chr14	6.40	532	60.38	细胞核 Nuclear
	Pbr005503.1	PbGT11	Chr12	6.36	536	60.58	细胞核 Nuclear
	Pbr027610.1	PbGT12	Chr7	5.76	566	65.15	细胞核 Nuclear
	Pbr038634.1	PbGT13	Chr6	5.65	758	82.46	细胞核 Nuclear
	Pbr010171.1	PbGT14	Chr14	5.57	647	71.99	细胞核 Nuclear
	Pbr010535.1	PbGT15	Chr5	6.60	572	64.69	细胞核 Nuclear
	Pbr036349.1	PbGT16	Chr10	8.73	534	61.13	细胞核 Nuclear
草莓	mrna29666	FvGT1	LG3	5.00	318	35.19	细胞核 Nuclear
Strawberry	mrna21007	FvGT2	LG7	8.43	284	32.41	细胞核 Nuclear
	mrna05400	FvGT3	LG6	9.78	378	40.84	细胞核 Nuclear
	mrna05956	FvGT4	LG6	4.68	395	45.27	细胞核 Nuclear
	mrna02091	FvGT5	LG1	4.87	364	42.27	细胞核 Nuclear
	mrna30101	FvGT6	LG6	6.81	591	64.60	细胞核 Nuclear
	mrna27722	FvGT7	LG5	6.55	376	43.32	细胞核 Nuclear
	mrna01828	FvGT8	LG5	5.56	769	83.55	细胞核 Nuclear
	mrna08173	FvGT9	LG2	6.21	578	65.76	细胞核 Nuclear
	mrna23617	FvGT10	LG7	6.19	433	49.00	细胞核 Nuclear
	mrna30156	FvGT11	LG6	6.42	579	65.77	细胞核 Nuclear
桃	Prupe.4G061800.1	PpGT1	Pp4	5.21	310	34.69	细胞核 Nuclear
Peach	Prupe.3G118000.1	PpGT2	Pp3	9.88	326	37.02	细胞核 Nuclear
	Prupe.2G253200.1	PpGT3	Pp2	9.38	548	61.78	叶绿体 Chloroplast
	Prupe.3G036000.1	PpGT4	Pp3	9.53	364	39.55	细胞核 Nuclear
	Prupe.3G071500.1	PpGT5	Pp3	4.59	398	45.72	细胞核 Nuclear
	Prupe.7G228600.1	PpGT6	Pp7	4.85	361	42.57	细胞核 Nuclear
	Prupe.7G120600.1	PpGT7	Pp7	6.41	527	57.10	细胞核 Nuclear
	Prupe.2G090800.1	PpGT8	Pp2	8.52	491	53.39	细胞核 Nuclear
	Prupe.1G235200.1	PpGT9	Pp1	5.90	380	43.75	细胞核 Nuclear
	Prupe.5G017700.1	PpGT10	Pp5	8.66	286	33.26	细胞核 Nuclear
	Prupe.7G116400.1	PpGT11	Pp7	6.40	544	61.86	细胞核 Nuclear
	Prupe.2G086500.1	PpGT12	Pp2	6.20	565	64.17	细胞核 Nuclear
	Prupe.5G137600.1	PpGT13	Pp5	5.26	776	84.46	细胞核 Nuclear
	Prupe.8G028800.1	PpGT14	Pp8	6.77	590	66.96	细胞核 Nuclear
	Prupe.8G028700.1	PpGT15	Pp8	6.05	630	70.57	细胞核 Nuclear
	Prupe.6G162600.1	PpGT16	Pp6	5.49	547	62.28	细胞核 Nuclear

物种 Species	基因编号 Gene ID	基因名称 Gene name	染色体 Chr	蛋白质Protein
物种 Species	基因编号 Gene ID	基因名称 Gene name	染色体 Chr	等电点 pI	长度/aa Length	分子质量/kD Molecular weight	亚细胞定位 Subcellular localization
梨	Pbr022283.1	PbGT1	Chr17	8.34	585	63.32	细胞核 Nuclear
Pear	Pbr027539.1	PbGT2	Chr9	9.61	350	38.01	细胞核 Nuclear
	Pbr009547.1	PbGT3	Chr1	9.27	247	27.90	细胞核 Nuclear
	Pbr010927.1	PbGT4	Chr7	9.20	241	27.34	细胞核 Nuclear
	Pbr016131.2	PbGT5	Chr10	5.50	448	49.17	细胞核 Nuclear
	Pbr034589.1	PbGT6	Chr5	4.70	398	45.36	细胞核 Nuclear
	Pbr027585.1	PbGT7	Chr2	4.79	363	42.82	细胞核 Nuclear
	Pbr015453.1	PbGT8	Chr15	4.90	360	42.54	细胞核 Nuclear
	Pbr036250.1	PbGT9	Chr16	5.95	426	48.87	细胞核 Nuclear
	Pbr016796.1	PbGT10	Chr14	6.40	532	60.38	细胞核 Nuclear
	Pbr005503.1	PbGT11	Chr12	6.36	536	60.58	细胞核 Nuclear
	Pbr027610.1	PbGT12	Chr7	5.76	566	65.15	细胞核 Nuclear
	Pbr038634.1	PbGT13	Chr6	5.65	758	82.46	细胞核 Nuclear
	Pbr010171.1	PbGT14	Chr14	5.57	647	71.99	细胞核 Nuclear
	Pbr010535.1	PbGT15	Chr5	6.60	572	64.69	细胞核 Nuclear
	Pbr036349.1	PbGT16	Chr10	8.73	534	61.13	细胞核 Nuclear
草莓	mrna29666	FvGT1	LG3	5.00	318	35.19	细胞核 Nuclear
Strawberry	mrna21007	FvGT2	LG7	8.43	284	32.41	细胞核 Nuclear
	mrna05400	FvGT3	LG6	9.78	378	40.84	细胞核 Nuclear
	mrna05956	FvGT4	LG6	4.68	395	45.27	细胞核 Nuclear
	mrna02091	FvGT5	LG1	4.87	364	42.27	细胞核 Nuclear
	mrna30101	FvGT6	LG6	6.81	591	64.60	细胞核 Nuclear
	mrna27722	FvGT7	LG5	6.55	376	43.32	细胞核 Nuclear
	mrna01828	FvGT8	LG5	5.56	769	83.55	细胞核 Nuclear
	mrna08173	FvGT9	LG2	6.21	578	65.76	细胞核 Nuclear
	mrna23617	FvGT10	LG7	6.19	433	49.00	细胞核 Nuclear
	mrna30156	FvGT11	LG6	6.42	579	65.77	细胞核 Nuclear
桃	Prupe.4G061800.1	PpGT1	Pp4	5.21	310	34.69	细胞核 Nuclear
Peach	Prupe.3G118000.1	PpGT2	Pp3	9.88	326	37.02	细胞核 Nuclear
	Prupe.2G253200.1	PpGT3	Pp2	9.38	548	61.78	叶绿体 Chloroplast
	Prupe.3G036000.1	PpGT4	Pp3	9.53	364	39.55	细胞核 Nuclear
	Prupe.3G071500.1	PpGT5	Pp3	4.59	398	45.72	细胞核 Nuclear
	Prupe.7G228600.1	PpGT6	Pp7	4.85	361	42.57	细胞核 Nuclear
	Prupe.7G120600.1	PpGT7	Pp7	6.41	527	57.10	细胞核 Nuclear
	Prupe.2G090800.1	PpGT8	Pp2	8.52	491	53.39	细胞核 Nuclear
	Prupe.1G235200.1	PpGT9	Pp1	5.90	380	43.75	细胞核 Nuclear
	Prupe.5G017700.1	PpGT10	Pp5	8.66	286	33.26	细胞核 Nuclear
	Prupe.7G116400.1	PpGT11	Pp7	6.40	544	61.86	细胞核 Nuclear
	Prupe.2G086500.1	PpGT12	Pp2	6.20	565	64.17	细胞核 Nuclear
	Prupe.5G137600.1	PpGT13	Pp5	5.26	776	84.46	细胞核 Nuclear
	Prupe.8G028800.1	PpGT14	Pp8	6.77	590	66.96	细胞核 Nuclear
	Prupe.8G028700.1	PpGT15	Pp8	6.05	630	70.57	细胞核 Nuclear
	Prupe.6G162600.1	PpGT16	Pp6	5.49	547	62.28	细胞核 Nuclear

复制基因对 Duplicated gene pairs	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	复制方式 Duplicated type
PbGT7/PbGT8	0.0333	0.1014	0.3284	片段复制 Segmental duplication
PbGT10/PbGT11	0.0329	0.1718	0.1915	片段复制 Segmental duplication
PbGT15/PbGT16	0.0646	0.1946	0.3320	片段复制 Segmental duplication