马铃薯bHLH转录因子家族全基因组鉴定与表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2020-1327

摘要/Abstract

摘要：

对马铃薯bHLH转录因子进行全基因组鉴定与表达模式分析,为其生物学功能研究提供借鉴。基于马铃薯基因组数据库和Pfam数据库,运用HMMER对马铃薯bHLH家族成员进行全基因组鉴定,剔除冗余序列后,利用ExPASy和MEME软件对候选序列进行基本理化性质及保守元件分析,并使用MEGA-X软件进行聚类分析;用MG2C和TBtools软件分别绘制染色体定位图和表达模式图。结果表明,从马铃薯基因组数据库中共检索出108个bHLH转录因子,其氨基酸数目为62-694个,分子量为7 527.78-75 939.94 Da,理论等电点为4.55-10.40。这些bHLH转录因子分布在马铃薯的12条染色体上,均具有典型的HLH结构域,可划分为16个亚族。基因表达模式分析表明,马铃薯bHLH家族成员具有组织表达特异性,多数响应盐、甘露醇、生长素、脱落酸、赤霉素及热等胁迫。马铃薯全基因组包括108个高度保守的bHLH基因家族成员,其表达具有组织特异性,并且响应非生物胁迫的诱导。

关键词: 马铃薯, bHLH转录因子, 全基因组鉴定, 胁迫, 表达分析

Abstract:

Genome-wide identification and expression pattern analysis of Solanum tuberosum bHLH transcription factor were conducted in order to provide reference for studying its biological function. Based on the S. tuberosum genome database and Pfam database,HMMER was used to identify the S. tuberosum bHLH family members through the whole genome. After the redundant sequences were excluded,ExPASy and MEME software were used to analyze the basic physicochemical properties and conservative element analysis of the candidate sequences. Further MEGA-X software was adapted for cluster analysis. MG2C and TBtools were employed to depict chromosome location and expression pattern respectively. As result,a total of 108 bHLH transcription factors were retrieved from the S. tuberosum genome database,the number of amino acids ranged from 62 to 694,the molecular weight was 7 527.78-75 939.94 Da,and the theoretical isoelectric point was 4.55-10.40. These bHLH transcription factors were distributed on 12 chromosomes of S. tuberosum,and all had typical HLH domain,which could be divided into 16 subgroups. Gene expression pattern analysis showed that S. tuberosum bHLH family members had tissue expression specificity and most of them responded to salt,mannitol,IAA,ABA,GA₃ and heat stress. The whole genome of S. tuberosum contains 108 highly conserved members of the bHLH gene family,whose expression is tissue specific and responds to the induction of abiotic stress.

Key words: Solanum tuberosum, bHLH transcription factor, genomic identification, stress, expression analysis

冯建英, 李立芹, 鲁黎明. 马铃薯bHLH转录因子家族全基因组鉴定与表达分析[J]. 生物技术通报, 2022, 38(2): 21-33.

FENG Jian-ying, LI Li-qin, LU Li-ming. Genome-wide Identification and Expression Analysis of the bHLH Transcription Factor Family in Solanum tuberosum[J]. Biotechnology Bulletin, 2022, 38(2): 21-33.

图/表 9

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基因 Gene	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
StbHLH2	ATGTTCACCGCCTTATTG	CTGATGAGATTAGAGCCACC
StbHLH14	CTAAAGGTGGAAGTGGGGTA	TTGGGGGTTGTCAATAAAAT
StbHLH15	ACAAGTTGCCCACCTACC	TGGAAGTTCTCACTGCCTCT
StbHLH34	AAAGGAACCGCCGCAAAC	GCGTCTTGGCTTCTAAGGATT
StbHLH39	ATCCTCTTGCTCGCCTGTT	GGAATAGTAGATTTTTGGGGCA
StbHLH53	ACCTCCTGTTCCGATGAT	ACCAAAGTTCCCTCCACT
StbHLH57	CATTGGATAAAGTCACCGATAC	CGAATCTACAGACGACCTCA
StbHLH59	GGCATTTTTCACGGTTGCCT	CCGTCGTCACTTCCCTATCG
StbHLH66	AGCACTTGTTCCTGGTTGTGA	AATGGTCCTTCCAAGCCACTC
StbHLH80	CCAGATTCACCCCGTCGTTT	CCTTGTGCTCACGAAACACC
StbHLH90	CCAGTTCCACTACACCGTCC	GCCGGAGGATTTGACGGAAT
StbHLH108	GTCAAATCGAAGAACACGCGG	CTGCGGCTTTCAGGGATAAGT

基因 Gene	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
StbHLH2	ATGTTCACCGCCTTATTG	CTGATGAGATTAGAGCCACC
StbHLH14	CTAAAGGTGGAAGTGGGGTA	TTGGGGGTTGTCAATAAAAT
StbHLH15	ACAAGTTGCCCACCTACC	TGGAAGTTCTCACTGCCTCT
StbHLH34	AAAGGAACCGCCGCAAAC	GCGTCTTGGCTTCTAAGGATT
StbHLH39	ATCCTCTTGCTCGCCTGTT	GGAATAGTAGATTTTTGGGGCA
StbHLH53	ACCTCCTGTTCCGATGAT	ACCAAAGTTCCCTCCACT
StbHLH57	CATTGGATAAAGTCACCGATAC	CGAATCTACAGACGACCTCA
StbHLH59	GGCATTTTTCACGGTTGCCT	CCGTCGTCACTTCCCTATCG
StbHLH66	AGCACTTGTTCCTGGTTGTGA	AATGGTCCTTCCAAGCCACTC
StbHLH80	CCAGATTCACCCCGTCGTTT	CCTTGTGCTCACGAAACACC
StbHLH90	CCAGTTCCACTACACCGTCC	GCCGGAGGATTTGACGGAAT
StbHLH108	GTCAAATCGAAGAACACGCGG	CTGCGGCTTTCAGGGATAAGT

基因 Gene	基因ID Gene ID	氨基酸数Number of amino acid	分子量 Molecular weight/Da	等电点 pI	基因 Gene	基因ID Gene ID	氨基酸数Number of amino acid	分子量 Molecular weight/Da	等电点 pI
StbHLH1	PGSC0003DMT400095438	295	33 008.42	8.21	StbHLH39	PGSC0003DMT400036951	551	59 473.80	5.78
StbHLH2	PGSC0003DMT400065029	397	43 515.43	6.16	StbHLH40	PGSC0003DMT400014656	276	31 123.90	5.76
StbHLH3	PGSC0003DMT400004497	471	53 156.01	5.18	StbHLH41	PGSC0003DMT400006783	311	34 469.88	6.45
StbHLH4	PGSC0003DMT400086863	393	44 510.14	6.01	StbHLH42	PGSC0003DMT400015377	203	22 928.51	9.69
StbHLH5	PGSC0003DMT400066807	464	50 747.96	7.62	StbHLH43	PGSC0003DMT400060615	224	25 030.63	7.56
StbHLH6	PGSC0003DMT400000652	598	66 369.87	6.86	StbHLH44	PGSC0003DMT400027293	235	27 571.74	8.82
StbHLH7	PGSC0003DMT400047220	452	49 967.36	5.61	StbHLH45	PGSC0003DMT400005446	345	38 526.03	5.87
StbHLH8	PGSC0003DMT400073574	337	38 301.38	5.14	StbHLH46	PGSC0003DMT400033589	321	35 634.69	4.55
StbHLH9	PGSC0003DMT400013074	353	39 806.96	6.33	StbHLH47	PGSC0003DMT400024185	204	22 750.35	9.88
StbHLH10	PGSC0003DMT400087143	333	36 913.79	5.28	StbHLH48	PGSC0003DMT400016360	338	37 784.66	4.66
StbHLH11	PGSC0003DMT400066257	305	34 150.70	7.11	StbHLH49	PGSC0003DMT400012591	382	41 627.38	6.33
StbHLH12	PGSC0003DMT400066259	307	34 354.03	6.67	StbHLH50	PGSC0003DMT400020534	314	34 098.61	5.32
StbHLH13	PGSC0003DMT400066261	304	33 738.26	7.14	StbHLH51	PGSC0003DMT400009603	406	44 073.59	7.66
StbHLH14	PGSC0003DMT400066264	307	34 179.83	7.12	StbHLH52	PGSC0003DMT400050572	321	35 928.50	5.11
StbHLH15	PGSC0003DMT400001888	442	49 692.41	5.65	StbHLH53	PGSC0003DMT400050585	520	56 513.05	5.21
StbHLH16	PGSC0003DMT400040021	303	34 207.55	6.54	StbHLH54	PGSC0003DMT400002155	312	34 997.42	6.00
StbHLH17	PGSC0003DMT400026937	326	36 823.76	5.23	StbHLH55	PGSC0003DMT400033757	210	23 748.34	8.89
StbHLH18	PGSC0003DMT400021383	244	27 458.61	5.56	StbHLH56	PGSC0003DMT400044959	231	26 357.79	5.64
StbHLH19	PGSC0003DMT400026449	235	26 275.12	8.64	StbHLH57	PGSC0003DMT400018046	578	64 285.91	7.61
StbHLH20	PGSC0003DMT400036021	442	49 217.42	5.90	StbHLH58	PGSC0003DMT400040761	390	44 069.48	5.27
StbHLH21	PGSC0003DMT400055910	267	29 914.13	7.80	StbHLH59	PGSC0003DMT400038134	515	56 408.13	5.13
StbHLH22	PGSC0003DMT400078776	317	35 038.85	6.12	StbHLH60	PGSC0003DMT400048941	312	35 241.59	4.72
StbHLH23	PGSC0003DMT400078675	335	38 417.26	5.44	StbHLH61	PGSC0003DMT400040448	225	25 610.16	7.62
StbHLH24	PGSC0003DMT400078696	347	39 529.70	6.39	StbHLH62	PGSC0003DMT400071861	62	7 527.78	10.4
StbHLH25	PGSC0003DMT400078698	209	23 532.27	6.17	StbHLH63	PGSC0003DMT400080418	260	28 511.99	7.81
StbHLH26	PGSC0003DMT400078699	323	35 931.15	5.47	StbHLH64	PGSC0003DMT400012487	390	42 992.79	5.76
StbHLH27	PGSC0003DMT400010253	376	41 285.79	5.04	StbHLH65	PGSC0003DMT400074075	530	57 936.63	5.31
StbHLH28	PGSC0003DMT400034838	296	32 476.68	5.27	StbHLH66	PGSC0003DMT400083164	416	46 807.69	8.71
StbHLH29	PGSC0003DMT400012997	335	38 164.49	5.23	StbHLH66	PGSC0003DMT400069569	284	31 977.18	6.76
StbHLH30	PGSC0003DMT400058169	268	30 772.88	7.63	StbHLH68	PGSC0003DMT400051980	467	51 763.96	7.19
StbHLH31	PGSC0003DMT400048857	148	16 910.86	9.75	StbHLH69	PGSC0003DMT400051674	477	52 903.87	6.59
StbHLH32	PGSC0003DMT400071293	224	25 544.12	8.60	StbHLH70	PGSC0003DMT400028917	444	46 271.20	6.09
StbHLH33	PGSC0003DMT400019550	214	24 405.08	8.94	StbHLH71	PGSC0003DMT400010463	252	28 629.96	4.97
StbHLH34	PGSC0003DMT400023497	355	38 301.12	5.94	StbHLH72	PGSC0003DMT400056685	374	42 308.55	8.80
StbHLH35	PGSC0003DMT400051137	338	37 637.08	6.08	StbHLH73	PGSC0003DMT400041156	517	57 437.21	7.09
StbHLH36	PGSC0003DMT400062844	291	30 828.06	5.65	StbHLH74	PGSC0003DMT400067287	351	39 693.02	8.14
StbHLH37	PGSC0003DMT400063026	536	58 417.99	7.35	StbHLH75	PGSC0003DMT400052622	255	27 880.55	6.92
StbHLH38	PGSC0003DMT400063117	437	48 174.88	6.79	StbHLH76	PGSC0003DMT400018274	224	25 831.73	6.32
StbHLH77	PGSC0003DMT400049504	485	52 745.68	6.07	StbHLH93	PGSC0003DMT400016793	348	36 847.65	8.57
StbHLH78	PGSC0003DMT400002963	598	65 258.62	5.92	StbHLH94	PGSC0003DMT400064399	388	42 575.81	5.83
StbHLH79	PGSC0003DMT400015017	456	51 791.64	6.22	StbHLH95	PGSC0003DMT400028057	389	44 514.29	5.88
StbHLH80	PGSC0003DMT400021165	435	49 379.65	5.89	StbHLH96	PGSC0003DMT400008370	198	22 043.97	8.88
StbHLH81	PGSC0003DMT400053651	319	36 510.05	4.85	StbHLH97	PGSC0003DMT400089728	305	34 320.40	5.48
StbHLH82	PGSC0003DMT400095303	311	35 808.26	4.90	StbHLH98	PGSC0003DMT400076759	180	20 751.84	9.58
StbHLH83	PGSC0003DMT400045210	330	36 732.34	6.10	StbHLH99	PGSC0003DMT400021130	360	39 675.21	5.92
StbHLH84	PGSC0003DMT400045204	694	75 939.94	5.47	StbHLH100	PGSC0003DMT400021062	380	41 565.47	9.10
StbHLH85	PGSC0003DMT400032139	360	40 669.07	6.81	StbHLH101	PGSC0003DMT400041644	237	27 276.91	5.27
StbHLH86	PGSC0003DMT400031899	431	48 790.06	6.71	StbHLH102	PGSC0003DMT400073760	262	30 275.48	5.87
StbHLH87	PGSC0003DMT400053639	492	53 992.33	7.13	StbHLH103	PGSC0003DMT400056716	441	48 896.06	6.65
StbHLH88	PGSC0003DMT400048756	578	62 943.67	6.42	StbHLH104	PGSC0003DMT400020244	382	39 561.65	6.21
StbHLH89	PGSC0003DMT400002512	284	31 495.30	5.46	StbHLH105	PGSC0003DMT400013766	272	31 224.18	6.76
StbHLH90	PGSC0003DMT400033569	590	64 760.08	5.81	StbHLH106	PGSC0003DMT400045820	296	33 899.60	7.02
StbHLH91	PGSC0003DMT400076223	285	32 950.42	6.27	StbHLH107	PGSC0003DMT400011651	413	46 698.70	5.92
StbHLH92	PGSC0003DMT400042791	439	49 242.61	6.06	StbHLH108	PGSC0003DMT400061284	489	54 218.28	5.12

基因 Gene	基因ID Gene ID	氨基酸数Number of amino acid	分子量 Molecular weight/Da	等电点 pI	基因 Gene	基因ID Gene ID	氨基酸数Number of amino acid	分子量 Molecular weight/Da	等电点 pI
StbHLH1	PGSC0003DMT400095438	295	33 008.42	8.21	StbHLH39	PGSC0003DMT400036951	551	59 473.80	5.78
StbHLH2	PGSC0003DMT400065029	397	43 515.43	6.16	StbHLH40	PGSC0003DMT400014656	276	31 123.90	5.76
StbHLH3	PGSC0003DMT400004497	471	53 156.01	5.18	StbHLH41	PGSC0003DMT400006783	311	34 469.88	6.45
StbHLH4	PGSC0003DMT400086863	393	44 510.14	6.01	StbHLH42	PGSC0003DMT400015377	203	22 928.51	9.69
StbHLH5	PGSC0003DMT400066807	464	50 747.96	7.62	StbHLH43	PGSC0003DMT400060615	224	25 030.63	7.56
StbHLH6	PGSC0003DMT400000652	598	66 369.87	6.86	StbHLH44	PGSC0003DMT400027293	235	27 571.74	8.82
StbHLH7	PGSC0003DMT400047220	452	49 967.36	5.61	StbHLH45	PGSC0003DMT400005446	345	38 526.03	5.87
StbHLH8	PGSC0003DMT400073574	337	38 301.38	5.14	StbHLH46	PGSC0003DMT400033589	321	35 634.69	4.55
StbHLH9	PGSC0003DMT400013074	353	39 806.96	6.33	StbHLH47	PGSC0003DMT400024185	204	22 750.35	9.88
StbHLH10	PGSC0003DMT400087143	333	36 913.79	5.28	StbHLH48	PGSC0003DMT400016360	338	37 784.66	4.66
StbHLH11	PGSC0003DMT400066257	305	34 150.70	7.11	StbHLH49	PGSC0003DMT400012591	382	41 627.38	6.33
StbHLH12	PGSC0003DMT400066259	307	34 354.03	6.67	StbHLH50	PGSC0003DMT400020534	314	34 098.61	5.32
StbHLH13	PGSC0003DMT400066261	304	33 738.26	7.14	StbHLH51	PGSC0003DMT400009603	406	44 073.59	7.66
StbHLH14	PGSC0003DMT400066264	307	34 179.83	7.12	StbHLH52	PGSC0003DMT400050572	321	35 928.50	5.11
StbHLH15	PGSC0003DMT400001888	442	49 692.41	5.65	StbHLH53	PGSC0003DMT400050585	520	56 513.05	5.21
StbHLH16	PGSC0003DMT400040021	303	34 207.55	6.54	StbHLH54	PGSC0003DMT400002155	312	34 997.42	6.00
StbHLH17	PGSC0003DMT400026937	326	36 823.76	5.23	StbHLH55	PGSC0003DMT400033757	210	23 748.34	8.89
StbHLH18	PGSC0003DMT400021383	244	27 458.61	5.56	StbHLH56	PGSC0003DMT400044959	231	26 357.79	5.64
StbHLH19	PGSC0003DMT400026449	235	26 275.12	8.64	StbHLH57	PGSC0003DMT400018046	578	64 285.91	7.61
StbHLH20	PGSC0003DMT400036021	442	49 217.42	5.90	StbHLH58	PGSC0003DMT400040761	390	44 069.48	5.27
StbHLH21	PGSC0003DMT400055910	267	29 914.13	7.80	StbHLH59	PGSC0003DMT400038134	515	56 408.13	5.13
StbHLH22	PGSC0003DMT400078776	317	35 038.85	6.12	StbHLH60	PGSC0003DMT400048941	312	35 241.59	4.72
StbHLH23	PGSC0003DMT400078675	335	38 417.26	5.44	StbHLH61	PGSC0003DMT400040448	225	25 610.16	7.62
StbHLH24	PGSC0003DMT400078696	347	39 529.70	6.39	StbHLH62	PGSC0003DMT400071861	62	7 527.78	10.4
StbHLH25	PGSC0003DMT400078698	209	23 532.27	6.17	StbHLH63	PGSC0003DMT400080418	260	28 511.99	7.81
StbHLH26	PGSC0003DMT400078699	323	35 931.15	5.47	StbHLH64	PGSC0003DMT400012487	390	42 992.79	5.76
StbHLH27	PGSC0003DMT400010253	376	41 285.79	5.04	StbHLH65	PGSC0003DMT400074075	530	57 936.63	5.31
StbHLH28	PGSC0003DMT400034838	296	32 476.68	5.27	StbHLH66	PGSC0003DMT400083164	416	46 807.69	8.71
StbHLH29	PGSC0003DMT400012997	335	38 164.49	5.23	StbHLH66	PGSC0003DMT400069569	284	31 977.18	6.76
StbHLH30	PGSC0003DMT400058169	268	30 772.88	7.63	StbHLH68	PGSC0003DMT400051980	467	51 763.96	7.19
StbHLH31	PGSC0003DMT400048857	148	16 910.86	9.75	StbHLH69	PGSC0003DMT400051674	477	52 903.87	6.59
StbHLH32	PGSC0003DMT400071293	224	25 544.12	8.60	StbHLH70	PGSC0003DMT400028917	444	46 271.20	6.09
StbHLH33	PGSC0003DMT400019550	214	24 405.08	8.94	StbHLH71	PGSC0003DMT400010463	252	28 629.96	4.97
StbHLH34	PGSC0003DMT400023497	355	38 301.12	5.94	StbHLH72	PGSC0003DMT400056685	374	42 308.55	8.80
StbHLH35	PGSC0003DMT400051137	338	37 637.08	6.08	StbHLH73	PGSC0003DMT400041156	517	57 437.21	7.09
StbHLH36	PGSC0003DMT400062844	291	30 828.06	5.65	StbHLH74	PGSC0003DMT400067287	351	39 693.02	8.14
StbHLH37	PGSC0003DMT400063026	536	58 417.99	7.35	StbHLH75	PGSC0003DMT400052622	255	27 880.55	6.92
StbHLH38	PGSC0003DMT400063117	437	48 174.88	6.79	StbHLH76	PGSC0003DMT400018274	224	25 831.73	6.32
StbHLH77	PGSC0003DMT400049504	485	52 745.68	6.07	StbHLH93	PGSC0003DMT400016793	348	36 847.65	8.57
StbHLH78	PGSC0003DMT400002963	598	65 258.62	5.92	StbHLH94	PGSC0003DMT400064399	388	42 575.81	5.83
StbHLH79	PGSC0003DMT400015017	456	51 791.64	6.22	StbHLH95	PGSC0003DMT400028057	389	44 514.29	5.88
StbHLH80	PGSC0003DMT400021165	435	49 379.65	5.89	StbHLH96	PGSC0003DMT400008370	198	22 043.97	8.88
StbHLH81	PGSC0003DMT400053651	319	36 510.05	4.85	StbHLH97	PGSC0003DMT400089728	305	34 320.40	5.48
StbHLH82	PGSC0003DMT400095303	311	35 808.26	4.90	StbHLH98	PGSC0003DMT400076759	180	20 751.84	9.58
StbHLH83	PGSC0003DMT400045210	330	36 732.34	6.10	StbHLH99	PGSC0003DMT400021130	360	39 675.21	5.92
StbHLH84	PGSC0003DMT400045204	694	75 939.94	5.47	StbHLH100	PGSC0003DMT400021062	380	41 565.47	9.10
StbHLH85	PGSC0003DMT400032139	360	40 669.07	6.81	StbHLH101	PGSC0003DMT400041644	237	27 276.91	5.27
StbHLH86	PGSC0003DMT400031899	431	48 790.06	6.71	StbHLH102	PGSC0003DMT400073760	262	30 275.48	5.87
StbHLH87	PGSC0003DMT400053639	492	53 992.33	7.13	StbHLH103	PGSC0003DMT400056716	441	48 896.06	6.65
StbHLH88	PGSC0003DMT400048756	578	62 943.67	6.42	StbHLH104	PGSC0003DMT400020244	382	39 561.65	6.21
StbHLH89	PGSC0003DMT400002512	284	31 495.30	5.46	StbHLH105	PGSC0003DMT400013766	272	31 224.18	6.76
StbHLH90	PGSC0003DMT400033569	590	64 760.08	5.81	StbHLH106	PGSC0003DMT400045820	296	33 899.60	7.02
StbHLH91	PGSC0003DMT400076223	285	32 950.42	6.27	StbHLH107	PGSC0003DMT400011651	413	46 698.70	5.92
StbHLH92	PGSC0003DMT400042791	439	49 242.61	6.06	StbHLH108	PGSC0003DMT400061284	489	54 218.28	5.12