被子植物小热激蛋白家族的比较基因组学分析

doi:10.11983/CBB20209

摘要/Abstract

摘要： 小热激蛋白(sHSP)是一类重要的响应外界环境变化以及调控植物生长发育的蛋白家族。基于在睡莲(Nymphaea colorata)、水稻(Oryza sativa)、拟南芥(Arabidopsis thaliana)和葡萄(Vitis vinifera)中分别鉴定到的33个NcsHSPs、24个OssHSPs、17个AtsHSPs和47个VvsHSPs, 表明sHSP家族可分为12个亚家族, 不同亚家族包含不同的sHSP成员数目、保守基序、基因结构以及复制基因数目。在4种模式被子植物的sHSP成员中共鉴定到12个基因复制事件, 片段复制事件和串联复制事件均与sHSP成员的扩增有关, 且片段复制事件发生的时间早于串联复制事件。在所有sHSP成员中, 拟南芥和葡萄的sHSP成员的同源性最高, 其次为睡莲和葡萄的sHSP成员。sHSP家族在被子植物中可能向更短的氨基酸长度、更小的分子量、更简单的基因结构以及更集中的染色体分布进化。此外, 在睡莲、水稻、拟南芥和葡萄中鉴定了一些可能与调控植物生长发育相关的候选基因。研究结果为4种模式被子植物sHSP家族的比较基因组学研究奠定了重要基础, 并为其它被子植物sHSP家族的研究提供重要参考。

关键词: sHSP家族, 比较基因组学, 扩增, 基因表达

Abstract: Small heat shock protein (sHSP) can respond to environmental stresses and regulate plant growth and development. In this study, 33 NcsHSPs, 24 OssHSPs, 17 AtsHSPs and 47 VvsHSPs were found in waterlily, rice, Arabidopsis, and grape, respectively. The sHSP family can be divided into 12 subfamilies, and different subfamily had different number of sHSP members, conserved motifs, gene structures and number of duplicated genes. Then, 12 gene duplication events in tle sHSP fanily were identified from 4 model angiosperms of sHSP family. The segmental and tandem duplication events were related to the gene expansion in the sHSP family, and the segmental duplication events occurred earlier than the tandem duplication events. Moreover, sHSP members in Arabidopsis and grape had the highest orthologous similarity, followed by sHSP members in waterlily and grape. Furthermore, sHSP family in angiosperms evolved towards sHSP members with smaller length of amino acid, lower molecular weight, simpler gene structure, and concentrated chromosomal localization. Besides, some sHSP members may be related to plant growth and development in waterlily, rice, Arabidopsis, and grape. Above all, these results could lay vital foundations on comparative genomics of the sHSP family in four model angiosperms and advance the sHSP family in other angiosperms.

Key words: sHSP family, comparative genomics, expansion, gene expression

范凯, 叶方婷, 毛志君, 潘鑫峰, 李兆伟, 林文雄. 被子植物小热激蛋白家族的比较基因组学分析. 植物学报, 2021, 56(3): 245-261.

Kai Fan, Fangting Ye, Zhijun Mao, Xinfeng Pan, Zhaowei Li, Wenxiong Lin. Comparative Genomics of the Small Heat Shock Protein Family in Angiosperms. Chinese Bulletin of Botany, 2021, 56(3): 245-261.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB20209

https://www.chinbullbotany.com/CN/Y2021/V56/I3/245

图/表 10

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Protein name	Locus name	Subfamily	Protein length (aa)	Molecular weight (kDa)	Theoretical pI	Instability index	Aliphatic index	GRAVY
NcsHSP01	GWHPAAYW001658	CI	60	6.64	9.16	41.10	99.00	-0.218
NcsHSP02	GWHPAAYW001878	CII	308	34.77	9.03	44.31	74.64	-0.624
NcsHSP03	GWHPAAYW002745	CV	276	30.85	4.88	44.78	77.36	-0.291
NcsHSP04	GWHPAAYW004666	PX	1189	132.46	5.86	44.51	85.53	-0.300
NcsHSP05	GWHPAAYW006130	ER	218	24.32	5.46	64.70	95.14	-0.411
NcsHSP06	GWHPAAYW006158	CII	378	43.02	8.36	50.40	74.76	-0.780
NcsHSP07	GWHPAAYW006159	CII	662	75.02	9.13	55.90	79.64	-0.665
NcsHSP08	GWHPAAYW006161	CII	314	35.79	8.86	47.40	79.39	-0.709
NcsHSP09	GWHPAAYW006746	CIII	164	18.56	5.75	53.09	81.28	-0.489
NcsHSP10	GWHPAAYW007213	CIV	132	14.36	6.83	58.83	82.80	-0.117
NcsHSP11	GWHPAAYW009125	CII	165	19.09	5.48	54.83	69.03	-0.921
NcsHSP12	GWHPAAYW010630	MTII	235	26.36	6.79	56.35	67.57	-0.687
NcsHSP13	GWHPAAYW010715	CI	129	15.42	9.12	60.26	59.53	-1.343
NcsHSP14	GWHPAAYW013759	CVI	154	17.47	5.57	46.32	73.96	-0.573
NcsHSP15	GWHPAAYW014339	CI	156	17.60	5.24	55.71	73.72	-0.552
NcsHSP16	GWHPAAYW014344	CI	158	18.29	8.92	54.19	74.05	-0.682
NcsHSP17	GWHPAAYW015449	MTI/CP	208	23.47	6.01	36.92	78.75	-0.667
NcsHSP18	GWHPAAYW018459	CI	833	94.56	6.14	53.05	69.45	-0.668
NcsHSP19	GWHPAAYW019072	CI	163	18.55	6.19	62.44	71.04	-0.601
NcsHSP20	GWHPAAYW019077	CI	337	37.62	7.83	57.71	78.66	-0.457

Protein name	Locus name	Subfamily	Protein length (aa)	Molecular weight (kDa)	Theoretical pI	Instability index	Aliphatic index	GRAVY
NcsHSP01	GWHPAAYW001658	CI	60	6.64	9.16	41.10	99.00	-0.218
NcsHSP02	GWHPAAYW001878	CII	308	34.77	9.03	44.31	74.64	-0.624
NcsHSP03	GWHPAAYW002745	CV	276	30.85	4.88	44.78	77.36	-0.291
NcsHSP04	GWHPAAYW004666	PX	1189	132.46	5.86	44.51	85.53	-0.300
NcsHSP05	GWHPAAYW006130	ER	218	24.32	5.46	64.70	95.14	-0.411
NcsHSP06	GWHPAAYW006158	CII	378	43.02	8.36	50.40	74.76	-0.780
NcsHSP07	GWHPAAYW006159	CII	662	75.02	9.13	55.90	79.64	-0.665
NcsHSP08	GWHPAAYW006161	CII	314	35.79	8.86	47.40	79.39	-0.709
NcsHSP09	GWHPAAYW006746	CIII	164	18.56	5.75	53.09	81.28	-0.489
NcsHSP10	GWHPAAYW007213	CIV	132	14.36	6.83	58.83	82.80	-0.117
NcsHSP11	GWHPAAYW009125	CII	165	19.09	5.48	54.83	69.03	-0.921
NcsHSP12	GWHPAAYW010630	MTII	235	26.36	6.79	56.35	67.57	-0.687
NcsHSP13	GWHPAAYW010715	CI	129	15.42	9.12	60.26	59.53	-1.343
NcsHSP14	GWHPAAYW013759	CVI	154	17.47	5.57	46.32	73.96	-0.573
NcsHSP15	GWHPAAYW014339	CI	156	17.60	5.24	55.71	73.72	-0.552
NcsHSP16	GWHPAAYW014344	CI	158	18.29	8.92	54.19	74.05	-0.682
NcsHSP17	GWHPAAYW015449	MTI/CP	208	23.47	6.01	36.92	78.75	-0.667
NcsHSP18	GWHPAAYW018459	CI	833	94.56	6.14	53.05	69.45	-0.668
NcsHSP19	GWHPAAYW019072	CI	163	18.55	6.19	62.44	71.04	-0.601
NcsHSP20	GWHPAAYW019077	CI	337	37.62	7.83	57.71	78.66	-0.457

Protein name	Locus name	Subfamily	Protein length (aa)	Molecular weight (kDa)	Theoretical pI	Instability index	Aliphatic index	GRAVY
NcsHSP21	GWHPAAYW019078	CI	156	17.38	5.69	54.61	75.00	-0.449
NcsHSP22	GWHPAAYW019481	CP	222	25.65	9.17	54.03	60.63	-0.880
NcsHSP23	GWHPAAYW022038	CI	159	18.24	5.60	65.94	69.18	-0.648
NcsHSP24	GWHPAAYW025914	CVI	160	18.57	5.82	41.67	70.00	-0.914
NcsHSP25	GWHPAAYW027820	ER	192	21.54	6.54	31.35	102.08	-0.202
NcsHSP26	GWHPAAYW027821	ER	676	74.58	5.31	41.90	85.41	-0.292
NcsHSP27	GWHPAAYW027823	ER	180	20.20	9.21	61.79	73.67	-0.636
NcsHSP28	GWHPAAYW027825	ER	191	21.24	7.93	29.89	91.41	-0.376
NcsHSP29	GWHPAAYW027826	ER	191	21.48	6.00	34.01	98.53	-0.246
NcsHSP30	GWHPAAYW027987	CP	226	25.18	6.65	50.88	75.88	-0.522
NcsHSP31	GWHPAAYW030961	ER	133	15.78	10.21	41.23	77.59	-0.929
NcsHSP32	GWHPAAYW030963	ER	126	14.05	5.63	37.53	109.13	-0.024
NcsHSP33	GWHPAAYW030964	ER	143	15.67	6.08	33.52	109.16	0.075
OssHSP01	LOC_Os01g04340.1	CI	150	16.65	6.31	34.230	77.200	-0.536
OssHSP02	LOC_Os01g04350.1	CI	166	17.89	4.96	55.210	87.590	0.051
OssHSP03	LOC_Os01g04360.1	CI	149	16.90	6.76	47.050	69.870	-0.648
OssHSP04	LOC_Os01g04370.1	CI	150	16.94	6.18	52.240	76.530	-0.605
OssHSP05	LOC_Os01g04380.1	CI	150	16.96	6.18	52.240	73.930	-0.617
OssHSP06	LOC_Os01g08860.1	CII	166	18.03	5.61	45.580	78.130	-0.386
OssHSP07	LOC_Os02g03570.1	CI	177	18.87	6.93	52.450	71.750	-0.406
OssHSP08	LOC_Os02g10710.1	MTII	219	23.59	7.74	47.270	86.030	-0.320
OssHSP09	LOC_Os02g12610.1	CII	175	19.02	5.73	39.010	84.060	-0.486
OssHSP10	LOC_Os02g48140.1	CVII	164	17.77	6.97	46.260	67.320	-0.534
OssHSP11	LOC_Os02g52150.1	MTI/CP	221	24.15	7.96	48.750	77.330	-0.519
OssHSP12	LOC_Os02g54140.1	CIII	172	18.60	7.85	40.550	77.150	-0.538
OssHSP13	LOC_Os03g14180.1	CP	240	26.66	6.78	53.350	75.120	-0.541
OssHSP14	LOC_Os03g15960.1	CI	161	17.91	5.79	57.860	64.780	-0.680
OssHSP15	LOC_Os03g16020.1	CI	154	17.37	6.18	49.280	66.430	-0.706
OssHSP16	LOC_Os03g16030.1	CI	161	18.08	6.77	58.690	61.680	-0.746
OssHSP17	LOC_Os03g16040.1	CI	159	17.66	6.18	55.510	66.790	-0.719
OssHSP18	LOC_Os04g36750.1	ER	215	23.23	5.34	35.060	82.650	-0.365
OssHSP19	LOC_Os05g23140.1	CP	251	27.64	9.42	39.120	69.240	-0.488
OssHSP20	LOC_Os05g42120.1	CV	203	22.28	4.82	54.030	69.800	-0.330
OssHSP21	LOC_Os06g11610.1	MTI/CP	248	26.23	5.27	43.470	79.270	-0.323
OssHSP22	LOC_Os06g14240.1	PX	146	16.02	8.13	36.730	84.790	-0.292
OssHSP23	LOC_Os07g33350.1	CIV	219	23.76	11.74	93.800	71.320	-0.642
OssHSP24	LOC_Os11g13980.1	ER	206	21.87	6.01	48.890	81.500	-0.126
AtsHSP01	AT1G07400.1	CI	157	17.83	5.99	43.380	70.060	-0.680
AtsHSP02	AT1G52560.1	MTII	232	26.54	6.86	45.660	68.880	-0.869
AtsHSP03	AT1G53540.1	CI	157	17.60	5.36	53.800	71.970	-0.578
AtsHSP04	AT1G54050.1	CIII	155	17.36	7.88	58.630	93.680	-0.504
AtsHSP05	AT1G59860.1	CI	155	17.62	6.85	50.240	70.970	-0.678
AtsHSP06	AT2G29500.1	CI	153	17.56	6.33	47.820	71.900	-0.720
AtsHSP07	AT3G46230.1	CI	156	17.44	5.20	46.980	68.590	-0.569

Protein name	Locus name	Subfamily	Protein length (aa)	Molecular weight (kDa)	Theoretical pI	Instability index	Aliphatic index	GRAVY
NcsHSP21	GWHPAAYW019078	CI	156	17.38	5.69	54.61	75.00	-0.449
NcsHSP22	GWHPAAYW019481	CP	222	25.65	9.17	54.03	60.63	-0.880
NcsHSP23	GWHPAAYW022038	CI	159	18.24	5.60	65.94	69.18	-0.648
NcsHSP24	GWHPAAYW025914	CVI	160	18.57	5.82	41.67	70.00	-0.914
NcsHSP25	GWHPAAYW027820	ER	192	21.54	6.54	31.35	102.08	-0.202
NcsHSP26	GWHPAAYW027821	ER	676	74.58	5.31	41.90	85.41	-0.292
NcsHSP27	GWHPAAYW027823	ER	180	20.20	9.21	61.79	73.67	-0.636
NcsHSP28	GWHPAAYW027825	ER	191	21.24	7.93	29.89	91.41	-0.376
NcsHSP29	GWHPAAYW027826	ER	191	21.48	6.00	34.01	98.53	-0.246
NcsHSP30	GWHPAAYW027987	CP	226	25.18	6.65	50.88	75.88	-0.522
NcsHSP31	GWHPAAYW030961	ER	133	15.78	10.21	41.23	77.59	-0.929
NcsHSP32	GWHPAAYW030963	ER	126	14.05	5.63	37.53	109.13	-0.024
NcsHSP33	GWHPAAYW030964	ER	143	15.67	6.08	33.52	109.16	0.075
OssHSP01	LOC_Os01g04340.1	CI	150	16.65	6.31	34.230	77.200	-0.536
OssHSP02	LOC_Os01g04350.1	CI	166	17.89	4.96	55.210	87.590	0.051
OssHSP03	LOC_Os01g04360.1	CI	149	16.90	6.76	47.050	69.870	-0.648
OssHSP04	LOC_Os01g04370.1	CI	150	16.94	6.18	52.240	76.530	-0.605
OssHSP05	LOC_Os01g04380.1	CI	150	16.96	6.18	52.240	73.930	-0.617
OssHSP06	LOC_Os01g08860.1	CII	166	18.03	5.61	45.580	78.130	-0.386
OssHSP07	LOC_Os02g03570.1	CI	177	18.87	6.93	52.450	71.750	-0.406
OssHSP08	LOC_Os02g10710.1	MTII	219	23.59	7.74	47.270	86.030	-0.320
OssHSP09	LOC_Os02g12610.1	CII	175	19.02	5.73	39.010	84.060	-0.486
OssHSP10	LOC_Os02g48140.1	CVII	164	17.77	6.97	46.260	67.320	-0.534
OssHSP11	LOC_Os02g52150.1	MTI/CP	221	24.15	7.96	48.750	77.330	-0.519
OssHSP12	LOC_Os02g54140.1	CIII	172	18.60	7.85	40.550	77.150	-0.538
OssHSP13	LOC_Os03g14180.1	CP	240	26.66	6.78	53.350	75.120	-0.541
OssHSP14	LOC_Os03g15960.1	CI	161	17.91	5.79	57.860	64.780	-0.680
OssHSP15	LOC_Os03g16020.1	CI	154	17.37	6.18	49.280	66.430	-0.706
OssHSP16	LOC_Os03g16030.1	CI	161	18.08	6.77	58.690	61.680	-0.746
OssHSP17	LOC_Os03g16040.1	CI	159	17.66	6.18	55.510	66.790	-0.719
OssHSP18	LOC_Os04g36750.1	ER	215	23.23	5.34	35.060	82.650	-0.365
OssHSP19	LOC_Os05g23140.1	CP	251	27.64	9.42	39.120	69.240	-0.488
OssHSP20	LOC_Os05g42120.1	CV	203	22.28	4.82	54.030	69.800	-0.330
OssHSP21	LOC_Os06g11610.1	MTI/CP	248	26.23	5.27	43.470	79.270	-0.323
OssHSP22	LOC_Os06g14240.1	PX	146	16.02	8.13	36.730	84.790	-0.292
OssHSP23	LOC_Os07g33350.1	CIV	219	23.76	11.74	93.800	71.320	-0.642
OssHSP24	LOC_Os11g13980.1	ER	206	21.87	6.01	48.890	81.500	-0.126
AtsHSP01	AT1G07400.1	CI	157	17.83	5.99	43.380	70.060	-0.680
AtsHSP02	AT1G52560.1	MTII	232	26.54	6.86	45.660	68.880	-0.869
AtsHSP03	AT1G53540.1	CI	157	17.60	5.36	53.800	71.970	-0.578
AtsHSP04	AT1G54050.1	CIII	155	17.36	7.88	58.630	93.680	-0.504
AtsHSP05	AT1G59860.1	CI	155	17.62	6.85	50.240	70.970	-0.678
AtsHSP06	AT2G29500.1	CI	153	17.56	6.33	47.820	71.900	-0.720
AtsHSP07	AT3G46230.1	CI	156	17.44	5.20	46.980	68.590	-0.569

Protein name	Locus name	Subfamily	Protein length (aa)	Molecular weight (kDa)	Theoretical pI	Instability index	Aliphatic index	GRAVY
AtsHSP08	AT4G10250.1	ER	195	22.00	5.58	36.450	93.950	-0.469
AtsHSP09	AT4G21870.1	CIV	134	15.39	5.17	73.930	93.810	-0.325
AtsHSP10	AT4G25200.1	MTI/CP	210	23.61	6.46	58.790	80.760	-0.649
AtsHSP11	AT4G27670.1	CP	227	25.34	8.49	46.860	72.070	-0.641
AtsHSP12	AT5G12020.1	CII	155	17.62	6.32	38.840	80.390	-0.617
AtsHSP13	AT5G12030.1	CII	156	17.69	5.59	44.370	75.000	-0.596
AtsHSP14	AT5G37670.1	PX	137	15.70	7.94	50.680	86.640	-0.512
AtsHSP15	AT5G51440.1	MTI/CP	210	23.47	8.96	52.510	84.000	-0.558
AtsHSP16	AT5G54660.1	CV	192	21.66	5.47	38.030	71.560	-0.500
AtsHSP17	AT5G59720.1	CI	161	18.13	6.77	48.090	67.200	-0.657
VvsHSP01	VIT_200s0707g00010.1	CIV	136	15.69	4.89	53.490	82.430	-0.315
VvsHSP02	VIT_200s0992g00020.1	CIV	136	15.70	5.01	54.190	82.430	-0.312
VvsHSP03	VIT_201s0010g02290.1	CP	226	25.56	6.77	48.710	62.170	-0.706
VvsHSP04	VIT_202s0154g00480.1	MTI/CP	201	22.45	9.24	45.150	77.060	-0.531
VvsHSP05	VIT_202s0154g00490.1	MTI/CP	201	22.55	9.11	51.710	75.670	-0.561
VvsHSP06	VIT_204s0008g01490.1	CII	156	17.34	5.94	41.520	82.500	-0.444
VvsHSP07	VIT_204s0008g01500.1	CII	152	16.69	6.84	42.090	79.540	-0.390
VvsHSP08	VIT_204s0008g01510.1	CII	156	17.40	5.77	44.190	76.220	-0.462
VvsHSP09	VIT_204s0008g01520.1	CII	156	17.58	5.58	40.180	78.080	-0.513
VvsHSP10	VIT_204s0008g01530.1	CII	480	53.16	8.89	39.780	68.600	-0.713
VvsHSP11	VIT_204s0008g01550.1	CII	156	17.41	5.94	39.580	71.790	-0.533
VvsHSP12	VIT_204s0008g01560.1	CII	113	12.66	8.66	38.840	83.540	-0.473
VvsHSP13	VIT_204s0008g01570.1	CII	166	18.60	5.95	40.640	68.670	-0.542
VvsHSP14	VIT_204s0008g01580.1	CII	156	17.42	6.62	42.220	76.790	-0.510
VvsHSP15	VIT_204s0008g01590.1	CII	155	17.29	5.94	37.610	81.030	-0.466
VvsHSP16	VIT_204s0008g01610.1	CII	158	18.14	6.33	40.180	75.820	-0.617
VvsHSP17	VIT_204s0008g01620.1	CII	159	18.42	8.46	42.080	83.900	-0.459
VvsHSP18	VIT_206s0004g05770.1	CI	144	16.31	6.93	33.000	75.070	-0.642
VvsHSP19	VIT_208s0058g00210.1	CI	148	16.88	5.81	64.560	66.490	-0.629
VvsHSP20	VIT_209s0002g00640.1	CIII	160	17.89	6.30	49.690	81.000	-0.516
VvsHSP21	VIT_209s0002g06790.1	MTII	233	26.31	7.78	53.870	82.060	-0.750
VvsHSP22	VIT_212s0035g01910.1	ER	250	28.39	7.94	49.940	89.400	-0.388
VvsHSP23	VIT_213s0019g00860.1	PX	142	15.81	6.75	51.850	85.000	-0.311
VvsHSP24	VIT_213s0019g02740.1	CI	151	17.17	5.81	46.350	74.110	-0.553
VvsHSP25	VIT_213s0019g02760.1	CI	140	15.80	6.77	42.530	72.290	-0.589
VvsHSP26	VIT_213s0019g02770.1	CI	151	17.10	5.81	48.460	72.850	-0.554
VvsHSP27	VIT_213s0019g02780.1	CI	151	17.02	5.80	45.690	70.260	-0.587
VvsHSP28	VIT_213s0019g02820.1	CI	151	17.12	5.81	47.080	70.260	-0.591
VvsHSP29	VIT_213s0019g02840.1	CI	151	17.09	5.54	50.220	72.850	-0.551
VvsHSP30	VIT_213s0019g02850.1	CI	151	17.05	5.80	45.440	70.260	-0.590
VvsHSP31	VIT_213s0019g02900.1	CI	108	12.64	6.18	52.990	80.190	-0.798
VvsHSP32	VIT_213s0019g02920.1	CI	136	15.27	5.70	46.020	79.490	-0.552
VvsHSP33	VIT_213s0019g02930.1	CI	160	18.17	6.78	53.430	76.690	-0.644
VvsHSP34	VIT_213s0019g03000.1	CI	160	18.15	7.93	55.700	76.690	-0.644