拟南芥花药绒毡层细胞中具有基因簇特征的基因进化和功能分析

doi:10.11983/CBB19103

摘要/Abstract

摘要： 在植物基因组中, 除了同源基因成簇现象外, 近年来还发现一些具有共表达特性的异源基因也能够以基因簇形式存在, 但这些异源基因簇的进化和生物学功能尚不清楚。花药发育和花粉形成是植物进化出的特有的生殖生物学过程, 同时产生了一些在花药绒毡层中特异表达和特定功能的基因簇基因。该研究通过筛选和分析花药绒毡层中基因簇基因的分子特性、表达调控、基因年龄和基因重复进化等信息, 探讨花药基因簇基因与植物开花功能进化之间的关系。结果表明, 在拟南芥(Arabidopsis thaliana)中共筛选到84个(13个基因簇)花药绒毡层特异高表达的基因簇基因, 它们主要产生于串联重复事件, 76%的基因出现在开花植物分化后的阶段, 主要参与生殖发育、花粉鞘组成和脂代谢等生物学过程。研究初步解析了拟南芥花药绒毡层中基因簇基因的基本特征、生物学功能和基因进化机制, 为深入揭示植物基因簇基因的遗传学功能奠定了基础。

关键词: 拟南芥, 基因簇, 花药绒毡层, 基因重复, 进化

Abstract: In plant genome, in addition to the discovery of homologous gene clustering, it has been known that some heterologous genes with co-expression characteristics can exist as gene clusters, however, the evolution and biological function of these heterogeneous gene clusters remain elusive. The development of anthers and the formation of pollen are unique reproductive biology processes evolved in seed plants. In this process, some gene cluster genes that specifically express and function in the anther tapetum are evolved. This study screened for some clustered genes expressed during anther development, and analyzed their molecular characteristics, expression regulation, gene age, as well as explored the relationship between the clustered genes and plant flowering function evolution. In Arabidopsis thaliana, we screened 84 clustered genes (which belong to 13 gene clusters), which are mainly expressed in tandem repeat events, and 76% of these genes appear in the latter stage of flowering plant evolution, that mainly involved in biological processes such as reproductive development, pollen sheath composition and lipid metabolism. This study has thus provided preliminary analysis on the basic characteristics, biological functions and mechanisms of the evolution of the clustered genes in the anther tapetum of Arabidopsis thaliana, which laid a foundation for future study on the function of the clustered genes.

Key words: Arabidopsis thaliana, gene cluster, anther tapetum, gene duplication, evolution

左泽远,刘琬琳,许杰. 拟南芥花药绒毡层细胞中具有基因簇特征的基因进化和功能分析. 植物学报, 2020, 55(2): 147-162.

Zeyuan Zuo,Wanlin Liu,Jie Xu. Evolution and Functional Analysis of Gene Clusters in Anther Tapetum Cells of Arabidopsis thaliana. Chinese Bulletin of Botany, 2020, 55(2): 147-162.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB19103

https://www.chinbullbotany.com/CN/Y2020/V55/I2/147

图/表 11

参考文献 37

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Cluster No.	AGI	MW (kDa)	PI	Location	TM	Description
1	AT1G12060	24786.8	9.09	Undefined	0	BCL-2-associated athanogene 5
1	AT1G12064	11961.3	9.24	Secreted	1	Unknown protein
1	AT1G12070	25456.4	4.52	Other	0	Immunoglobulin E-set superfamily protein
1	AT1G12080	15381.7	3.74	Undefined	0	Vacuolar calcium-binding protein-related
1	AT1G12090	13912.3	8.15	Secreted	0	Extensin-like protein
1	AT1G12100	13909.2	6.90	Secreted	0	Bifunctional inhibitor/lipid-transfer protein/seed storage
1	AT1G12110	64921.2	8.57	Other	11	Nitrate transporter 1.1
2	AT1G61560	67225.5	10.06	Undefined	8	Seven transmembrane MLO family protein
2	AT1G61563	8906.4	9.93	Secreted	1	Ralf-like 8
2	AT1G61566	8259.6	9.93	Secreted	1	Ralf-like 9
2	AT1G61570	9411.6	5.03	Undefined	0	Translocase of the inner mitochondrial membrane 13
2	AT1G61575	5641.3	4.50	Undefined	0	Unknown protein
3	AT1G74540	56740.6	8.36	Undefined	1	Cytochrome P450, family 98
3	AT1G74550	55418.9	8.88	Undefined	0	Cytochrome P450, family 98
4	AT1G75880	41333.3	8.23	Secreted	1	SGNH hydrolase-type esterase
4	AT1G75890	42126.2	8.44	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75900	39815.4	5.47	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75910	37910.6	10.30	Secreted	0	Extracellular lipase 4
4	AT1G75920	39254.5	10.06	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75930	38595.7	9.89	Secreted	0	Extracellular lipase 6
4	AT1G75940	61674.7	6.04	Secreted	1	Glycosyl hydrolase superfamily protein
5	AT2G47010	55049.8	6.50	Secreted	0	Unknown protein
5	AT2G47020	46827.8	7.36	Mitochondrion	0	Peptide chain release factor 1
5	AT2G47030	64137.1	9.44	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47040	64727.7	9.32	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47050	23775.5	9.35	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47060	43753.3	7.67	Other	0	Protein kinase superfamily protein
6	AT3G07810	52055.5	8.81	Other	0	RNA-binding (RRM/RBD/RNP motifs) family protein
6	AT3G07820	41681.1	7.34	Secreted	1	Pectin lyase-like superfamily protein
6	AT3G07830	42912.9	8.69	Secreted	0	Pectin lyase-like superfamily protein
6	AT3G07840	42591.5	8.08	Secreted	0	Pectin lyase-like superfamily protein
6	AT3G07850	45599.9	8.43	Secreted	1	Pectin lyase-like superfamily protein
6	AT3G07860	18672.5	10.45	Other	0	Ubiquitin-like superfamily protein
7	AT3G28730	71645.6	5.56	Undefined	0	High mobility group
7	AT3G28740	57691.8	9.23	Secreted	1	Cytochrome P450 superfamily protein
7	AT3G28750	35478.4	10.45	Secreted	0	Unknown protein
7	AT3G28760	49598.7	6.72	Undefined	0	Unknown protein
7	AT3G28770	232851.8	4.73	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28780	61329	3.92	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28790	62765.8	10.04	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28810	47872.2	9.70	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28820	47786	9.38	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28830	55500.6	10.42	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28840	36875.3	10.06	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28850	48178.4	4.72	Undefined	0	Glutaredoxin family protein
7	AT3G28860	136786.9	8.37	Other	10	ATP binding cassette subfamily B19
8	AT4G29290	8554.9	6.92	Secreted	1	Low-molecular-weight cysteine-rich 26
8	AT4G29300	8510.8	4.40	Secreted	1	Low-molecular-weight cysteine-rich 27
8	AT4G29305	8359.7	7.91	Secreted	1	Low-molecular-weight cysteine-rich 25
8	AT4G29310	45655.6	9.63	Undefined	0	Protein of unknown function (DUF1005)
8	AT4G29330	29213.2	10.33	Other	6	DERLIN-1
8	AT4G29340	14418.3	4.84	Other	0	Profilin 4
8	AT4G29350	13997.8	4.67	Other	0	Profilin 2
9	AT5G07410	39336.9	8.70	Secreted	1	Pectin lyase-like superfamily protein
9	AT5G07420	39658	9.40	Secreted	0	Pectin lyase-like superfamily protein
9	AT5G07430	39910.3	9.11	Secreted	0	Pectin lyase-like superfamily protein
9	AT5G07440	44698.7	6.51	Undefined	0	Glutamate dehydrogenase 2
9	AT5G07450	25004.5	6.01	Undefined	0	Cyclin p4;3
10	AT5G07510	18462.4	12.43	Secreted	3	Glycine-rich protein 14
10	AT5G07520	21482.5	10.55	Secreted	3	Glycine-rich protein 18
10	AT5G07530	53192.9	11.13	Undefined	3	Glycine rich protein 17
10	AT5G07540	22300.1	10.85	Secreted	3	Glycine-rich protein 16
10	AT5G07550	10682.5	10.13	Secreted	2	Glycine-rich protein 19
10	AT5G07560	15458.3	11.20	Other	3	Glycine-rich protein 20
10	AT5G07570	148459.7	3.36	Secreted	10	Glycine/proline-rich protein
11	AT5G17450	16995.5	10.18	Undefined	0	Heavy metal transport/detoxification
11	AT5G17460	35918.8	8.34	Undefined	0	Unknown protein
11	AT5G17470	16320.1	4.01	Other	0	EF hand calcium-binding protein family
11	AT5G17480	9048	4.30	Other	0	Pollen calcium-binding protein 1
11	AT5G17490	57326.1	4.49	Other	0	RGA-like protein 3
11	AT5G17500	59551	8.19	Secreted	1	Glycosyl hydrolase superfamily protein
12	AT5G53800	41786.3	10.38	Other	0	Unknown protein
12	AT5G53810	41944.2	5.17	Other	0	O-methyltransferase family protein
12	AT5G53820	7028.7	10.26	Undefined	0	Late embryogenesis abundant protein (LEA) family protein
12	AT5G53830	26918.8	10.18	Undefined	0	VQ motif-containing protein
12	AT5G53840	50906.6	7.31	Other	0	F-box/RNI-like/FBD-like domains-containing pro- tein
12	AT5G53850	56520.1	6.14	Undefined	0	Haloacid dehalogenase-like hydrolase family protein
13	AT5G67460	41995.4	8.16	Secreted	0	O-glycosyl hydrolases family 17 protein
13	AT5G67470	98648.8	9.91	Secreted	2	Formin homolog 6
13	AT5G67480	43817.7	9.59	Undefined	0	BTB and TAZ domain protein 4
13	AT5G67490	11869.8	4.25	Undefined	0	Unknown protein
13	AT5G67500	32904.9	7.68	Other	0	Voltage dependent anion channel 2
13	AT5G67510	16790.3	11.74	Undefined	0	Translation protein SH3-like family protein
13	AT5G67520	34064.3	9.29	Undefined	0	Adenosine-5'-phosphosulfate (APS) kinase 4

Cluster No.	AGI	MW (kDa)	PI	Location	TM	Description
1	AT1G12060	24786.8	9.09	Undefined	0	BCL-2-associated athanogene 5
1	AT1G12064	11961.3	9.24	Secreted	1	Unknown protein
1	AT1G12070	25456.4	4.52	Other	0	Immunoglobulin E-set superfamily protein
1	AT1G12080	15381.7	3.74	Undefined	0	Vacuolar calcium-binding protein-related
1	AT1G12090	13912.3	8.15	Secreted	0	Extensin-like protein
1	AT1G12100	13909.2	6.90	Secreted	0	Bifunctional inhibitor/lipid-transfer protein/seed storage
1	AT1G12110	64921.2	8.57	Other	11	Nitrate transporter 1.1
2	AT1G61560	67225.5	10.06	Undefined	8	Seven transmembrane MLO family protein
2	AT1G61563	8906.4	9.93	Secreted	1	Ralf-like 8
2	AT1G61566	8259.6	9.93	Secreted	1	Ralf-like 9
2	AT1G61570	9411.6	5.03	Undefined	0	Translocase of the inner mitochondrial membrane 13
2	AT1G61575	5641.3	4.50	Undefined	0	Unknown protein
3	AT1G74540	56740.6	8.36	Undefined	1	Cytochrome P450, family 98
3	AT1G74550	55418.9	8.88	Undefined	0	Cytochrome P450, family 98
4	AT1G75880	41333.3	8.23	Secreted	1	SGNH hydrolase-type esterase
4	AT1G75890	42126.2	8.44	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75900	39815.4	5.47	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75910	37910.6	10.30	Secreted	0	Extracellular lipase 4
4	AT1G75920	39254.5	10.06	Secreted	0	GDSL-like lipase/Acylhydrolase
4	AT1G75930	38595.7	9.89	Secreted	0	Extracellular lipase 6
4	AT1G75940	61674.7	6.04	Secreted	1	Glycosyl hydrolase superfamily protein
5	AT2G47010	55049.8	6.50	Secreted	0	Unknown protein
5	AT2G47020	46827.8	7.36	Mitochondrion	0	Peptide chain release factor 1
5	AT2G47030	64137.1	9.44	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47040	64727.7	9.32	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47050	23775.5	9.35	Secreted	1	Plant invertase/pectin methylesterase inhibitor superfamily protein
5	AT2G47060	43753.3	7.67	Other	0	Protein kinase superfamily protein
6	AT3G07810	52055.5	8.81	Other	0	RNA-binding (RRM/RBD/RNP motifs) family protein
6	AT3G07820	41681.1	7.34	Secreted	1	Pectin lyase-like superfamily protein
6	AT3G07830	42912.9	8.69	Secreted	0	Pectin lyase-like superfamily protein
6	AT3G07840	42591.5	8.08	Secreted	0	Pectin lyase-like superfamily protein
6	AT3G07850	45599.9	8.43	Secreted	1	Pectin lyase-like superfamily protein
6	AT3G07860	18672.5	10.45	Other	0	Ubiquitin-like superfamily protein
7	AT3G28730	71645.6	5.56	Undefined	0	High mobility group
7	AT3G28740	57691.8	9.23	Secreted	1	Cytochrome P450 superfamily protein
7	AT3G28750	35478.4	10.45	Secreted	0	Unknown protein
7	AT3G28760	49598.7	6.72	Undefined	0	Unknown protein
7	AT3G28770	232851.8	4.73	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28780	61329	3.92	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28790	62765.8	10.04	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28810	47872.2	9.70	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28820	47786	9.38	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28830	55500.6	10.42	Secreted	1	Protein of unknown function (DUF1216)
7	AT3G28840	36875.3	10.06	Secreted	0	Protein of unknown function (DUF1216)
7	AT3G28850	48178.4	4.72	Undefined	0	Glutaredoxin family protein
7	AT3G28860	136786.9	8.37	Other	10	ATP binding cassette subfamily B19
8	AT4G29290	8554.9	6.92	Secreted	1	Low-molecular-weight cysteine-rich 26
8	AT4G29300	8510.8	4.40	Secreted	1	Low-molecular-weight cysteine-rich 27
8	AT4G29305	8359.7	7.91	Secreted	1	Low-molecular-weight cysteine-rich 25
8	AT4G29310	45655.6	9.63	Undefined	0	Protein of unknown function (DUF1005)
8	AT4G29330	29213.2	10.33	Other	6	DERLIN-1
8	AT4G29340	14418.3	4.84	Other	0	Profilin 4
8	AT4G29350	13997.8	4.67	Other	0	Profilin 2
9	AT5G07410	39336.9	8.70	Secreted	1	Pectin lyase-like superfamily protein
9	AT5G07420	39658	9.40	Secreted	0	Pectin lyase-like superfamily protein
9	AT5G07430	39910.3	9.11	Secreted	0	Pectin lyase-like superfamily protein
9	AT5G07440	44698.7	6.51	Undefined	0	Glutamate dehydrogenase 2
9	AT5G07450	25004.5	6.01	Undefined	0	Cyclin p4;3
10	AT5G07510	18462.4	12.43	Secreted	3	Glycine-rich protein 14
10	AT5G07520	21482.5	10.55	Secreted	3	Glycine-rich protein 18
10	AT5G07530	53192.9	11.13	Undefined	3	Glycine rich protein 17
10	AT5G07540	22300.1	10.85	Secreted	3	Glycine-rich protein 16
10	AT5G07550	10682.5	10.13	Secreted	2	Glycine-rich protein 19
10	AT5G07560	15458.3	11.20	Other	3	Glycine-rich protein 20
10	AT5G07570	148459.7	3.36	Secreted	10	Glycine/proline-rich protein
11	AT5G17450	16995.5	10.18	Undefined	0	Heavy metal transport/detoxification
11	AT5G17460	35918.8	8.34	Undefined	0	Unknown protein
11	AT5G17470	16320.1	4.01	Other	0	EF hand calcium-binding protein family
11	AT5G17480	9048	4.30	Other	0	Pollen calcium-binding protein 1
11	AT5G17490	57326.1	4.49	Other	0	RGA-like protein 3
11	AT5G17500	59551	8.19	Secreted	1	Glycosyl hydrolase superfamily protein
12	AT5G53800	41786.3	10.38	Other	0	Unknown protein
12	AT5G53810	41944.2	5.17	Other	0	O-methyltransferase family protein
12	AT5G53820	7028.7	10.26	Undefined	0	Late embryogenesis abundant protein (LEA) family protein
12	AT5G53830	26918.8	10.18	Undefined	0	VQ motif-containing protein
12	AT5G53840	50906.6	7.31	Other	0	F-box/RNI-like/FBD-like domains-containing pro- tein
12	AT5G53850	56520.1	6.14	Undefined	0	Haloacid dehalogenase-like hydrolase family protein
13	AT5G67460	41995.4	8.16	Secreted	0	O-glycosyl hydrolases family 17 protein
13	AT5G67470	98648.8	9.91	Secreted	2	Formin homolog 6
13	AT5G67480	43817.7	9.59	Undefined	0	BTB and TAZ domain protein 4
13	AT5G67490	11869.8	4.25	Undefined	0	Unknown protein
13	AT5G67500	32904.9	7.68	Other	0	Voltage dependent anion channel 2
13	AT5G67510	16790.3	11.74	Undefined	0	Translation protein SH3-like family protein
13	AT5G67520	34064.3	9.29	Undefined	0	Adenosine-5'-phosphosulfate (APS) kinase 4

Phylostratum	WGD	Tandem	Proximal	Dispersed	Singleton
PS13	0	0	0	0	0
PS12	0	0	0	0	0
PS11	4 (21.05%)	13 (32.50%)	0	1 (5.00%)	0
PS10	4 (21.05%)	2 (5.00%)	0	1 (5.00%)	1 (25.00%)
PS9	7 (36.84%)	15 (37.50%)	0	11 (55.00%)	2 (50.00%)
PS8	0	1 (2.50%)	0	0	0
PS7	1 (5.26%)	0	0	1 (5.00%)	0
PS6	0	0	0	0	0
PS5	0	0	0	0	0
PS4	0	0	0	0	0
PS3	0	0	0	0	0
PS2	3 (15.79%)	7 (17.50%)	0	6 (30.00%)	0
PS1	0	2 (5.00%)	1 (100%)	0	1 (25.00%)

Phylostratum	WGD	Tandem	Proximal	Dispersed	Singleton
PS13	0	0	0	0	0
PS12	0	0	0	0	0
PS11	4 (21.05%)	13 (32.50%)	0	1 (5.00%)	0
PS10	4 (21.05%)	2 (5.00%)	0	1 (5.00%)	1 (25.00%)
PS9	7 (36.84%)	15 (37.50%)	0	11 (55.00%)	2 (50.00%)
PS8	0	1 (2.50%)	0	0	0
PS7	1 (5.26%)	0	0	1 (5.00%)	0
PS6	0	0	0	0	0
PS5	0	0	0	0	0
PS4	0	0	0	0	0
PS3	0	0	0	0	0
PS2	3 (15.79%)	7 (17.50%)	0	6 (30.00%)	0
PS1	0	2 (5.00%)	1 (100%)	0	1 (25.00%)