茉莉花TCP基因家族全基因组鉴定及其表达分析

doi:10.7668/hbnxb.20194408

摘要/Abstract

摘要：

为探讨茉莉花TCP基因家族在其生长发育过程中的作用,基于茉莉花的基因组数据,利用生物信息学方法对茉莉花TCP(JsTCP)基因进行了全基因组鉴定及分析,并分析了TCP基因家族在花发育不同时期和花粉-柱头互作中的表达水平。结果显示,茉莉花全基因组中共鉴定出27个TCP基因家族成员,命名为JsTCP1~JsTCP25,其蛋白包含208~539个氨基酸残基,分子量为22.95~56.96 ku,等电点为5.70~9.97,均为不稳定的亲水性蛋白。亚细胞定位预测结果显示,JsTCPs均位于细胞核内。染色体定位结果显示,JsTCPs不均匀分布在10条染色体上。基因结构分析结果显示,JsTCPs具有1~5个外显子以及0~4个内含子。蛋白保守基序和系统进化分析结果显示,JsTCPs均含保守的TCP结构域,可分为Class Ⅰ和Class Ⅱ 2个亚类。启动子顺式作用元件的分析结果显示,JsTCPs启动子上含有多个植物激素响应、胁迫响应和生长发育相关等元件。表达模式分析结果显示,24个JsTCPs基因在茉莉花花发育不同时期表达,22个基因在花粉-柱头互作中表达。总之,本研究鉴定了27个茉莉花TCP基因家族成员,并发现家族成员在花发育不同时期和授粉后不同时期特异表达。

关键词: 茉莉花, TCP基因家族, 全基因组鉴定, 系统进化分析, 表达分析

Abstract:

To explore the function of the TCP gene family in the growth and development of Jasminum sambac,bioinformatics methods were used to identify and analyze the whole genome of J.sambac TCP(JsTCP)gene family.Moreover,the expression levels of TCP gene family in different stages of flower development and pollen-stigma interaction were analyzed.A total of 27 TCP gene family members were identified from the whole genome of J.sambac,named JsTCP1—JsTCP25.The protein contained 208—539 amino acid residues,with molecular weight of 22.95—56.96 ku and isoelectric point of 5.70—9.97,and all of them were unstable hydrophilic proteins.The subcellular localization prediction showed that all JsTCPs were located in the nucleus.JsTCPs were unevenly distributed on 10 chromosomes.Gene structure analysis showed that JsTCPs had 1—5 exons and 0—4 introns.Protein conserved motifs and phylogenetic analysis showed that JsTCPs contained conserved TCP domain,and they were divided into two subclasses:Class Ⅰ and Class Ⅱ.Promoter of JsTCPs contained cis-acting elements related to plant hormone response,stress response,and growth and development.The expression pattern analysis showed that 24 JsTCPs were expressed at different stages of flower development,and 22 genes were expressed in pollen-stigma interactions.In conclusion,27 TCP gene family members were identified from J.sambac,and it found that they expressed specifically at different stages of flower development and different stages after pollination.

Key words: Jasmine, TCP gene family, Genome-wide identification, Phylogenetic analysis, Expression analysis

齐香玉, 李新茹, 陈双双, 冯景, 陈慧杰, 金玉妍, 苗艳华, 邓衍明. 茉莉花TCP基因家族全基因组鉴定及其表达分析[J]. 华北农学报, 2024, 39(1): 63-71. doi: 10.7668/hbnxb.20194408.

QI Xiangyu, LI Xinru, CHEN Shuangshuang, FENG Jing, CHEN Huijie, JIN Yuyan, MIAO Yanhua, DENG Yanming. Genome-wide Identification of TCP Gene Family in Jasminum sambac and Expression Analysis Involved in Flower Development and Pollen-pistil Interaction[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(1): 63-71. doi: 10.7668/hbnxb.20194408.

http://www.hbnxb.net/CN/Y2024/V39/I1/63

图/表 8

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基因名称 Gene name	基因号 Gene ID	基因组定位 Gene location	外显子个数 Number of exon	氨基酸数量/aa Number of amino acid	分子量/ku Molecular weight	等电点 Isoelectric point (pI)	不稳定系数 Instability index	平均亲水性 Average hydropathicity	亚细胞定位 Subcellular location
JsTCP1	chr4.g3220	chr4:44428553—44429335(-)	1	260	29.25	9.46	55.85	-0.647	细胞核
JsTCP2	chr1.g1128	chr1:11521466—11523648(-)	3	488	52.75	9.12	48.59	-0.725	细胞核
JsTCP3	chr3.g2263	chr3:38290019—38290942(+)	1	307	34.40	7.96	56.01	-0.749	细胞核
JsTCP4	chr13.g2204	chr13:32149211—32150527(+)	1	438	47.79	6.32	57.57	-0.802	细胞核
JsTCP5	chr4.g2600	chr4:30549262—30549888(+)	1	208	23.46	9.48	61.84	-0.638	细胞核
JsTCP6a	chr2.g2843	chr2:42768357—42769430(-)	1	357	38.55	7.93	62.42	-0.562	细胞核
JsTCP6b	chr2.g2864	chr2:42884976—42886049(-)	1	357	38.53	7.93	63.17	-0.556	细胞核
JsTCP7	chr4.g2626	chr4:30958353—30964556(+)	5	388	41.83	9.85	50.14	-0.415	细胞核
JsTCP8	chr6.g256	chr6:2926045—2927286(-)	1	413	43.67	6.88	49.02	-0.710	细胞核
JsTCP9	chr5.g929	chr5:7521384—7522268(-)	1	294	31.03	9.00	57.92	-0.352	细胞核
JsTCP10	chr13.g1726	chr13:28107959—28108771(-)	1	270	30.26	5.72	51.40	-0.781	细胞核
JsTCP11	chr4.g1908	chr4:20354907—20355551(+)	1	214	22.95	9.61	64.13	-0.244	细胞核
JsTCP12	chr9.g1921	chr9:33927672—33928652(+)	1	326	37.40	9.26	45.32	-0.807	细胞核
JsTCP13	chr7.g1644	chr7:30145798—30146775(-)	1	325	36.54	8.78	55.29	-0.725	细胞核
JsTCP14	chr1.g784	chr1:7660570—7661712(+)	1	380	40.76	6.74	59.59	-0.656	细胞核
JsTCP15	chr2.g1807	chr2:32679099—32680154(+)	1	351	37.30	8.61	64.57	-0.604	细胞核
JsTCP16	chr9.g2216	chr9:38745953—38746864(-)	1	303	32.01	9.07	59.94	-0.498	细胞核
JsTCP17	chr7.g417	chr7:6331686—6332606(+)	1	306	34.58	9.18	62.97	-0.745	细胞核
JsTCP18	chr7.g2341	chr7:36871144—36871966(+)	2	237	26.63	9.78	47.69	-0.939	细胞核
JsTCP19	chr3.g1880	chr3:35160637—35161800(-)	1	387	40.70	6.67	65.73	-0.408	细胞核
JsTCP20	chr4.g803	chr4:9531479—9532393(+)	1	304	32.57	7.95	60.63	-0.762	细胞核
JsTCP21	chr4.g2627	chr4:30983295—30986035(+)	2	332	36.17	8.96	58.82	-0.482	细胞核
JsTCP22	chr5.g285	chr5:2053649—2055419(-)	2	539	56.96	6.70	58.25	-0.674	细胞核
JsTCP23	chr10.g724	chr10:9196963—9198153(-)	1	396	45.15	5.70	43.19	-0.979	细胞核
JsTCP24	chr3.g3279	chr3:50522901—50524148(+)	1	415	45.24	8.59	56.15	-0.823	细胞核
JsTCP25a	chr7.g1554	chr7:29134169—29134996(+)	1	275	31.05	9.97	65.12	-0.624	细胞核
JsTCP25b	chr7.g1555	chr7:29148099—29148929(+)	1	276	31.52	9.28	51.95	-0.649	细胞核

基因名称 Gene name	基因号 Gene ID	基因组定位 Gene location	外显子个数 Number of exon	氨基酸数量/aa Number of amino acid	分子量/ku Molecular weight	等电点 Isoelectric point (pI)	不稳定系数 Instability index	平均亲水性 Average hydropathicity	亚细胞定位 Subcellular location
JsTCP1	chr4.g3220	chr4:44428553—44429335(-)	1	260	29.25	9.46	55.85	-0.647	细胞核
JsTCP2	chr1.g1128	chr1:11521466—11523648(-)	3	488	52.75	9.12	48.59	-0.725	细胞核
JsTCP3	chr3.g2263	chr3:38290019—38290942(+)	1	307	34.40	7.96	56.01	-0.749	细胞核
JsTCP4	chr13.g2204	chr13:32149211—32150527(+)	1	438	47.79	6.32	57.57	-0.802	细胞核
JsTCP5	chr4.g2600	chr4:30549262—30549888(+)	1	208	23.46	9.48	61.84	-0.638	细胞核
JsTCP6a	chr2.g2843	chr2:42768357—42769430(-)	1	357	38.55	7.93	62.42	-0.562	细胞核
JsTCP6b	chr2.g2864	chr2:42884976—42886049(-)	1	357	38.53	7.93	63.17	-0.556	细胞核
JsTCP7	chr4.g2626	chr4:30958353—30964556(+)	5	388	41.83	9.85	50.14	-0.415	细胞核
JsTCP8	chr6.g256	chr6:2926045—2927286(-)	1	413	43.67	6.88	49.02	-0.710	细胞核
JsTCP9	chr5.g929	chr5:7521384—7522268(-)	1	294	31.03	9.00	57.92	-0.352	细胞核
JsTCP10	chr13.g1726	chr13:28107959—28108771(-)	1	270	30.26	5.72	51.40	-0.781	细胞核
JsTCP11	chr4.g1908	chr4:20354907—20355551(+)	1	214	22.95	9.61	64.13	-0.244	细胞核
JsTCP12	chr9.g1921	chr9:33927672—33928652(+)	1	326	37.40	9.26	45.32	-0.807	细胞核
JsTCP13	chr7.g1644	chr7:30145798—30146775(-)	1	325	36.54	8.78	55.29	-0.725	细胞核
JsTCP14	chr1.g784	chr1:7660570—7661712(+)	1	380	40.76	6.74	59.59	-0.656	细胞核
JsTCP15	chr2.g1807	chr2:32679099—32680154(+)	1	351	37.30	8.61	64.57	-0.604	细胞核
JsTCP16	chr9.g2216	chr9:38745953—38746864(-)	1	303	32.01	9.07	59.94	-0.498	细胞核
JsTCP17	chr7.g417	chr7:6331686—6332606(+)	1	306	34.58	9.18	62.97	-0.745	细胞核
JsTCP18	chr7.g2341	chr7:36871144—36871966(+)	2	237	26.63	9.78	47.69	-0.939	细胞核
JsTCP19	chr3.g1880	chr3:35160637—35161800(-)	1	387	40.70	6.67	65.73	-0.408	细胞核
JsTCP20	chr4.g803	chr4:9531479—9532393(+)	1	304	32.57	7.95	60.63	-0.762	细胞核
JsTCP21	chr4.g2627	chr4:30983295—30986035(+)	2	332	36.17	8.96	58.82	-0.482	细胞核
JsTCP22	chr5.g285	chr5:2053649—2055419(-)	2	539	56.96	6.70	58.25	-0.674	细胞核
JsTCP23	chr10.g724	chr10:9196963—9198153(-)	1	396	45.15	5.70	43.19	-0.979	细胞核
JsTCP24	chr3.g3279	chr3:50522901—50524148(+)	1	415	45.24	8.59	56.15	-0.823	细胞核
JsTCP25a	chr7.g1554	chr7:29134169—29134996(+)	1	275	31.05	9.97	65.12	-0.624	细胞核
JsTCP25b	chr7.g1555	chr7:29148099—29148929(+)	1	276	31.52	9.28	51.95	-0.649	细胞核

旁系同源基因对 Paralogs pairs	非同义突变频率 Ka	同义突变频率 Ks	Ka/Ks
JsTCP6a-JsTCP6b	0.001 236	0.003 841	0.321 663
JsTCP25a-JsTCP25b	0.091 672	0.159 519	0.574 678

旁系同源基因对 Paralogs pairs	非同义突变频率 Ka	同义突变频率 Ks	Ka/Ks
JsTCP6a-JsTCP6b	0.001 236	0.003 841	0.321 663
JsTCP25a-JsTCP25b	0.091 672	0.159 519	0.574 678

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