龙眼TCP家族全基因组鉴定与表达分析

doi:10.16420/j.issn.0513-353x.2020-0717

摘要/Abstract

摘要：

利用生物信息学方法对龙眼TCP（DlTCP）基因家族进行全基因组鉴定,通过实时荧光定量PCR（qRT-PCR）技术分析龙眼TCP基因家族成员体胚发生早期表达模式及其对ABA和MeJA的响应模式。从龙眼基因组数据库中共鉴定获得20个龙眼TCP成员。这些DlTCP蛋白包含169 ~ 540个不等的氨基酸残基,分子量介于39.6 ~ 57.2 kD之间,理论等电点介于5.90 ~ 9.45。亚细胞定位预测显示,18个成员在细胞核中。染色体定位显示,DlTCP分布在龙眼15条染色体中的11条染色体上;共线性分析发现有12个DlTCP基因参与片段复制事件。启动子顺式作用元件分析显示,DlTCP成员启动子序列上含有响应激素应答、调控生长发育的元件。系统进化分析可将DlTCP分为2类,均具有典型TCP结构域。体胚发生早期表达模式分析表明,DlTCP2/4a/4b/13/17/18/19/23均在胚性愈伤组织阶段高表达,DlTCP5b/

关键词: 龙眼, TCP转录因子, 成员鉴定, ABA, MeJA, 实时荧光定量PCR

Abstract:

To study the potential function of longan TCP gene family,bioinformatics methods were used to perform the genome-wide identification of family in Dimocarpus longan TCP genes（DlTCP）. The expression patterns of DlTCP in longan somatic embryo development and their responses to ABA and MeJA were detected by the real-time quantitative PCR（qRT-PCR）. In this study,20 longan TCP gene family members were identified in the longan genome database. These DlTCP proteins contained 169- 540 amino acid residues,with molecular weights ranging from 39.6 kD to 57.2 kD,and theoretical isoelectric points ranging from 5.90-9.45. The prediction of subcellular localization showed that 18 members were located in the nucleus. DlTCP were distributed on 11 of the 15 chromosomes of longan. Synteny analysis revealed that 12 of DlTCP were involved in fragment replication events. Promoter cis-acting elements analysis showed that DlTCP family members contained hormone response cis-acting elements and regulate growth and development cis-acting elements. The longan TCP family members can be divided into two categories in phylogenetic evolution,and they all had typical TCP domains. QRT-PCR results showed that DlTCP2/4a/4b/13/17/18/19/23 were highly expressed in the embryogenic callus（EC）stage,DlTCP5b/8 were highly expressed in the incomplete compact pro-embrogenic cultures（IcpEC）stage,and only DlTCP20a was highly expressed in the globular embryos（GE）stage,indicating that the higly expression of DlTCP may contribute to the morphogenesis of early somatic embryos in longan. In addition,the family members also exhibited different expression patterns after exogenous hormones treatments. After exogenous ABA induction,the expression of four DlTCP members was significantly down regulated,and four were up-regulated;After MeJA induction,the expression of three members was significantly down-regulated and four up-regulated,indicating that DlTCP members can respond to ABA and MeJA.

Key words: Dimocarpus longan, TCP transcription factor, gene famliy identification, ABA, MeJA, qRT-PCR

中图分类号:

S667.2

蒋梦琦, 薛晓东, 苏立遥, 陈燕, 张舒婷, 李晓斐, 王培育, 张梓浩, 赖钟雄, 林玉玲. 龙眼TCP家族全基因组鉴定与表达分析[J]. 园艺学报, 2021, 48(12): 2481-2496.

JIANG Mengqi, XUE Xiaodong, SU Liyao, CHEN Yan, ZHANG Shuting, LI Xiaofei, WANG Peiyu, ZHANG Zihao, LAI Zhongxiong, LIN Yuling. Genome-wide Identification and Expression Analysis of TCP Family in Dimocarpus longan[J]. Acta Horticulturae Sinica, 2021, 48(12): 2481-2496.

图/表 11

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基因名称 Gene name	基因ID Gene ID	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
DlTCP1	Dlo030081	TGATCTCCAGGACATGCTAGG	TGCACATCTTTTCTCTGGTCC
DlTCP2	Dlo021979	CTGTGGAGTTGGATGGTGAAG	GACACTACCAATACCACCAGTCAG
DlTCP4a	Dlo009059	CAATGGGTGCTTCAAACGAC	CCAGCATCATAACCAAGTGGAG
DlTCP4b	Dlo027391	CGTGGCACCCGAATATTAGT	AGTTGATTGATGAGGTCGTGG
DlTCP5b	Dlo031128	CTCATGATCCGAACACCTCTC	CCAGTAGCTAACCATTCTTCCTTAC
DlTCP8	Dlo024507	TCAGGTGAAGCGGTCGAC	CATAGGGACCCGGATGATG
DlTCP9	Dlo012848	CGGAGCCAGCTATTATTGC	GTTGTGGCACCATGAAGAAC
DlTCP11	Dlo029447	CTAACTCACTCCTCCCCGTTAC	ACCCTACAAGACACCGACG
DlTCP13	Dlo030148	CATCATTCAATGTCATCTTCT	TCAATCCATGGCTGCCTAAT
DlTCP15	Dlo018528	TCCATAACCGGCGATGAC	GCTCGACCCTGAACTCCTTA
DlTCP17	Dlo026163	AGAACGCCGTGTCACCTT	TGTTACTCATTCCAGGCGG
DlTCP18	Dlo031253	ACATGGCCGATTCAACAAG	AACACTCACGCAGCTGCT
DlTCP19	Dlo019709	GCACCGATCACACCAATGT	TGCTACTCGAACTGGAACTGG
DlTCP20a	Dlo019007	GCTGAGCCATCTATAATTGCTG	CACTCCCATAACTTGATGCC
DlTCP20b	Dlo027551	GAAGCCAGCAGAGATCAAAGAT	GGTATGGTTCCACTCCCTGT
DlTCP21	Dlo017839	GAGAATCCGGATGCCAAT	TTGTGATCCAGTGAAGTCGAG
DlTCP23	Dlo014979	CCCACCACGAGAACAGTG	GTAAGGAGACGTTAAGGGAGG
Fe-SOD		GGTCAGATGGTGAAGCCGTAGAG	GTCTATGCCACCGATACAACAAACCC

基因名称 Gene name	基因ID Gene ID	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
DlTCP1	Dlo030081	TGATCTCCAGGACATGCTAGG	TGCACATCTTTTCTCTGGTCC
DlTCP2	Dlo021979	CTGTGGAGTTGGATGGTGAAG	GACACTACCAATACCACCAGTCAG
DlTCP4a	Dlo009059	CAATGGGTGCTTCAAACGAC	CCAGCATCATAACCAAGTGGAG
DlTCP4b	Dlo027391	CGTGGCACCCGAATATTAGT	AGTTGATTGATGAGGTCGTGG
DlTCP5b	Dlo031128	CTCATGATCCGAACACCTCTC	CCAGTAGCTAACCATTCTTCCTTAC
DlTCP8	Dlo024507	TCAGGTGAAGCGGTCGAC	CATAGGGACCCGGATGATG
DlTCP9	Dlo012848	CGGAGCCAGCTATTATTGC	GTTGTGGCACCATGAAGAAC
DlTCP11	Dlo029447	CTAACTCACTCCTCCCCGTTAC	ACCCTACAAGACACCGACG
DlTCP13	Dlo030148	CATCATTCAATGTCATCTTCT	TCAATCCATGGCTGCCTAAT
DlTCP15	Dlo018528	TCCATAACCGGCGATGAC	GCTCGACCCTGAACTCCTTA
DlTCP17	Dlo026163	AGAACGCCGTGTCACCTT	TGTTACTCATTCCAGGCGG
DlTCP18	Dlo031253	ACATGGCCGATTCAACAAG	AACACTCACGCAGCTGCT
DlTCP19	Dlo019709	GCACCGATCACACCAATGT	TGCTACTCGAACTGGAACTGG
DlTCP20a	Dlo019007	GCTGAGCCATCTATAATTGCTG	CACTCCCATAACTTGATGCC
DlTCP20b	Dlo027551	GAAGCCAGCAGAGATCAAAGAT	GGTATGGTTCCACTCCCTGT
DlTCP21	Dlo017839	GAGAATCCGGATGCCAAT	TTGTGATCCAGTGAAGTCGAG
DlTCP23	Dlo014979	CCCACCACGAGAACAGTG	GTAAGGAGACGTTAAGGGAGG
Fe-SOD		GGTCAGATGGTGAAGCCGTAGAG	GTCTATGCCACCGATACAACAAACCC

基因名称 Gene name	基因ID Gene ID	染色体 Chr	基因组定位 Gene location	开放阅读框 ORF/bp	氨基酸数 Amino acid number	分子量 Molecular weight	理论等电点 pI	不稳定系数 Instability index	亚细胞定位 Subcellular location
DlTCP1	Dlo030081	14	12715538:12717415	1 062	353	39 513.21	9.41	52.04	细胞核Nucleus
DlTCP2	Dlo021979	10	8735823:8746343	1 512	503	55 328.04	8.42	54.23	细胞核Nucleus
DlTCP4a	Dlo009059	4	10439106:10441967	1 251	416	45 292.48	6.35	56.10	细胞核Nucleus
DlTCP4b	Dlo027391	13	5039037:5042408	1 065	354	38 741.10	6.22	49.13	细胞核Nucleus
DlTCP5a	Dlo026162	12	19976189:19976698	510	169	39 613.57	8.62	42.30	细胞核Nucleus
DlTCP5b	Dlo031128	15	7294709:7295881	1 173	390	43 679.68	9.00	53.05	细胞核Nucleus
DlTCP8	Dlo024507	11	17156563:17158185	1 623	540	57 211.58	6.62	61.62	细胞核Nucleus
DlTCP9	Dlo012848	5	32302987:32304165	1 179	392	41 341.56	8.97	52.88	细胞核Nucleus
DlTCP11	Dlo029447	14	5931490:5932119	630	209	22 462.23	8.82	74.76	细胞核Nucleus
DlTCP12	Dlo018254	8	18820036:18821397	1 362	453	49 819.29	9.10	53.43	细胞核Nucleus
DlTCP13	Dlo030148	14	13720270:13723613	1 029	342	37 824.36	8.42	56.72	细胞核Nucleus
DlTCP14	Dlo032223	15	18165748:18167034	1 287	428	46 492.80	7.54	63.63	细胞核Nucleus
DlTCP15	Dlo018528	8	21299710:21300948	1 239	412	44 078.51	7.35	57.80	细胞核Nucleus
DlTCP17	Dlo026163	12	19984109:19984681	573	190	20 595.15	6.29	37.10	叶绿体Chloroplast
DlTCP18	Dlo031253	15	8846922:8847980	1 059	352	39 608.05	7.27	49.95	细胞核Nucleus
DlTCP19	Dlo019709	9	5138059:5139069	1 011	336	36 084.09	5.9	59.25	细胞核Nucleus
DlTCP20a	Dlo019007	8	25450145:25450999	855	284	30 303.73	9.01	44.23	细胞核Nucleus
DlTCP20b	Dlo027551	13	6380380:6382053	1 152	383	41 510.79	9.06	56.77	线粒体 Mitochondrion
DlTCP21	Dlo017839	8	12941326:12942114	789	262	27 391.62	9.45	39.31	细胞核Nucleus
DlTCP23	Dlo014979	6	25244640:25245548	909	302	32 075.54	7.17	51.82	细胞核Nucleus

基因名称 Gene name	基因ID Gene ID	染色体 Chr	基因组定位 Gene location	开放阅读框 ORF/bp	氨基酸数 Amino acid number	分子量 Molecular weight	理论等电点 pI	不稳定系数 Instability index	亚细胞定位 Subcellular location
DlTCP1	Dlo030081	14	12715538:12717415	1 062	353	39 513.21	9.41	52.04	细胞核Nucleus
DlTCP2	Dlo021979	10	8735823:8746343	1 512	503	55 328.04	8.42	54.23	细胞核Nucleus
DlTCP4a	Dlo009059	4	10439106:10441967	1 251	416	45 292.48	6.35	56.10	细胞核Nucleus
DlTCP4b	Dlo027391	13	5039037:5042408	1 065	354	38 741.10	6.22	49.13	细胞核Nucleus
DlTCP5a	Dlo026162	12	19976189:19976698	510	169	39 613.57	8.62	42.30	细胞核Nucleus
DlTCP5b	Dlo031128	15	7294709:7295881	1 173	390	43 679.68	9.00	53.05	细胞核Nucleus
DlTCP8	Dlo024507	11	17156563:17158185	1 623	540	57 211.58	6.62	61.62	细胞核Nucleus
DlTCP9	Dlo012848	5	32302987:32304165	1 179	392	41 341.56	8.97	52.88	细胞核Nucleus
DlTCP11	Dlo029447	14	5931490:5932119	630	209	22 462.23	8.82	74.76	细胞核Nucleus
DlTCP12	Dlo018254	8	18820036:18821397	1 362	453	49 819.29	9.10	53.43	细胞核Nucleus
DlTCP13	Dlo030148	14	13720270:13723613	1 029	342	37 824.36	8.42	56.72	细胞核Nucleus
DlTCP14	Dlo032223	15	18165748:18167034	1 287	428	46 492.80	7.54	63.63	细胞核Nucleus
DlTCP15	Dlo018528	8	21299710:21300948	1 239	412	44 078.51	7.35	57.80	细胞核Nucleus
DlTCP17	Dlo026163	12	19984109:19984681	573	190	20 595.15	6.29	37.10	叶绿体Chloroplast
DlTCP18	Dlo031253	15	8846922:8847980	1 059	352	39 608.05	7.27	49.95	细胞核Nucleus
DlTCP19	Dlo019709	9	5138059:5139069	1 011	336	36 084.09	5.9	59.25	细胞核Nucleus
DlTCP20a	Dlo019007	8	25450145:25450999	855	284	30 303.73	9.01	44.23	细胞核Nucleus
DlTCP20b	Dlo027551	13	6380380:6382053	1 152	383	41 510.79	9.06	56.77	线粒体 Mitochondrion
DlTCP21	Dlo017839	8	12941326:12942114	789	262	27 391.62	9.45	39.31	细胞核Nucleus
DlTCP23	Dlo014979	6	25244640:25245548	909	302	32 075.54	7.17	51.82	细胞核Nucleus