种子植物抗细胞凋亡DAD基因的演化

doi:10.11983/CBB16137

摘要/Abstract

摘要： 抗细胞凋亡基因(DAD)是一个高度保守的细胞凋亡抑制基因, 在植物生长发育中承担重要功能。为全面了解DAD基因在种子植物中的分布和演化规律, 该文利用31种植物的全基因组数据, 通过生物信息学手段, 深入探讨和分析了不同植物类群中DAD基因的拷贝数目、基因结构和染色体定位, 并综合另外7种裸子植物的转录组数据探讨了其在种子植物中的演化趋势。结果表明, DAD基因属于低拷贝基因, 在不同种子植物中只具有1-3个拷贝; 不同DAD基因编码的氨基酸长度在108-170 aa之间变动。同线性和系统发育分析进一步表明, 种子植物DAD基因的演化具有明显的谱系特异性。随机复制和染色体大片段复制及其随后的基因丢失可能是其维持低拷贝的重要方式。

关键词: 染色体定位, DAD, 复制类型, 全基因组, 基因结构

Abstract: Defender against apoptotic death (DAD) is a highly conserved cellular apoptosis gene and plays an important role in seed plant growth and development. To fully understand the evolutionary pattern of the DAD gene in seed plants, based on the whole genome data of 31 plants, we analyzed copy number, structure, chromosome location of the DAD genes by using bioinformatics. In addition, along with transcriptome data for seven gymnosperms, we discuss the evolutionary trend of the genes in seed plants. The DAD gene is a low-copy gene with only 1-3 copies in different seed plants, and the length of different DAD protein varies from 108 to 170 aa. Phylogenetic and syntonic analyses further showed that the evolution of the DAD gene in these seed species has a lineage-specific characteristic. Random and block duplication and subsequent gene loss were possibly important ways to maintain the low-copy number of DAD genes in seed plant genomes.

Key words: chromosome location, DAD, duplication pattern, whole genome, gene structure

包颖, 梅玉芹. 种子植物抗细胞凋亡DAD基因的演化. 植物学报, 2017, 52(5): 590-597.

Ying Bao, Yuqin Mei. Evolution of Defender Against Apoptotic Death (DAD) Genes in Seed Plants. Chinese Bulletin of Botany, 2017, 52(5): 590-597.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB16137

https://www.chinbullbotany.com/CN/Y2017/V52/I5/590

图/表 2

参考文献 20

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Taxa	Gene ID	Strand	Chromosome	Duplication pattern	Gene structure		Amino acid (aa)
Taxa	Gene ID	Strand	Chromosome	Duplication pattern	Intron	Exon	Amino acid (aa)
Angiosperm
Dicot
Arabidopsis lyrata	AL1G33450	_	Scaffold_1	Block	4	5	115
	AL4G20890	+	Scaffold_4	Block	4	5	116
A. thaliana	AT1G32210	_	Chr01	Block	4	5	115
	AT2G35520	+	Chr02	Block	4	5	116
Brassica rapa	BR05G20160	+	ChrA05	Block	4	5	115
	BR09G26700^a	+	ChrA09	Block	6	7	201 (88) ^d
Capsella rubella	CRU_001G29110	_	Scaffold_1	Block	4	5	115
	CRU_004G16620	+	Scaffold_4	Block	4	5	115
Citrullus lanatus	CL10G00840	+	Chr10		4	5	115
Cucumis melo	CM00021G01290	_	Scaffold00021		4	5	115
Eucalyptus grandis	EG0008G05930	+	Scaffold_8		4	5	115
Fragaria vesca	FV2G07670	+	LG2		4	5	124
Gossypium raimondii	GR03G18540	+	Chr03	Block	4	5	117
	GR08G22400	_	Chr08	Block	4	5	117
Malus domestica	MD05G025840	+	Chr05	Random	4	5	119
	MD10G000120	+	Chr10	Random	4	5	119
Manihot esculenta	ME04430G00010	+	Scaffold04430	Random	4	5	115
	ME07304G00010	+	Scaffold07304	Random	4	5	115
Populus trichocarpa	PT01G13680	_	Chr01	Block	4	5	115
	PT03G09680	+	Chr03	Block	4	5	115
Prunus persica	PPE_004G33460	_	Scaffold_4	Block	4	5	119
	PPE_008G00790	_	Scaffold_8	Block	4	5	119
Ricinus communis	RC29634G00390	+	29634	Random	4	5	115
	RC30068G01440	+	30068	Random	4	5	113
Solanum lycopersicum	SL08G076460	+	Chr08		4	5	116
S. tuberosum	ST08G008690	_	Chr08	Block	4	5	116
	ST08G021840	_	Chr08	Block	4	5	116
Thellungiella parvula	TP1G27890	_	Chr1-1		4	5	115
Theobroma cacao	TC0003G30500	+	Scaffold_3		4	5	116
Vitis vinifera	VV02G01690	+	Chr02		4	5	115
Moncot
Brachypodium distachyon	BD1G50180	+	Chr01		4	5	114
Hordeum vulgare	HV1571041G00020	_	Contig_1571041	Random	4	5	114
	HV44460G00030	+	Contig_44460	Random	4	5	114
Oryza sativa	OS04G32550	+	Chr04		4	5	114
Setaria italica	SI004G00880	+	Scaffold_4		4	5	114
Sorghum bicolor	SB10G001000	+	Chr10		4	5	114
Zea mays	ZM09G06480	_	Chr09		4	5	114
Musa acuminata	MA07G17850	_	Chr07	Block	4	5	115
	MA10G06540^b	_	Chr10	Block	-	1	48 (22)^d
	MA11G08020	+	Chr11	Block	4	5	170
Basal taxon
Amborella trichopoda	ATR_00025G00360	+	Scaffold00025		4	5	121
Gymnosperm
Taxa
Ginkgo biloba^c Gnetum montanum^c	Gene ID	Strand	Chromosome	Duplication pattern	Gene structure		Amino acid (aa)
Ginkgo biloba^c Gnetum montanum^c	Gene ID	Strand	Chromosome	Duplication pattern	Intron	Exon	Amino acid (aa)
Picea abies	GBI00024938	+	6973		-	-	123
	GMO00028447	_	GTHK-0066600		-	-	113
	PAB00021420^a	_	MA_128105	Random	5	6	162 (67)^d
P. glauca^c	PAB00041636	_	MA_42912	Random	4	5	115
	PAB00057214^b	+	MA_8328929	Random	1	2	50 (45)^d
	PGL00020840	+	PUT-39823 PUT-39823		-	-	115
P. sitchensis^c	PGL00013662	+	PUT-23726 PUT-23726		-	-	115
	PGL00010558	+	PUT-16509		-	-	115
Pinus pinaster^c	PSI00016644	+	PUT-531483		-	-	148
	PSI00008404	+	PUT-21837		-	-	115
Pi. sylvestris^c	PPI00061658	_	Unigene30039		-	-	115
	PPI00006515	_	Cotig25413		-	-	115
	PSY00006071	_	Isotig31028		-	-	115
Pi. taeda	PSY00026421	+	Isotig68699		-	-	115
	PSY00004335	+	isotig24244		-	-	115
	PTA00003657	_	Scaffold464	Random	4	5	115
Pseudotsuga menziesii ^c	PTA00022345^b	+	Scaffold214279	Random	2	3	86 (72)^d
	PTA00022344^b	+	Scaffold214279	Random	1	2	44 (44)^d
Moss Physcomitrella patens	PME00105748	+	Psme_598296871		-	-	146
Moss Physcomitrella patens	PME00105747	+	Psme_598296869		-	-	115
Alga Chlamydomonas reinhardtii	PP00045G01180	+	Scaffold_45		4	5	131
Alga Chlamydomonas reinhardtii	PP00456G00180	-	Scaffold_456		4	5	114

Taxa	Gene ID	Strand	Chromosome	Duplication pattern	Gene structure		Amino acid (aa)
Taxa	Gene ID	Strand	Chromosome	Duplication pattern	Intron	Exon	Amino acid (aa)
Angiosperm
Dicot
Arabidopsis lyrata	AL1G33450	_	Scaffold_1	Block	4	5	115
	AL4G20890	+	Scaffold_4	Block	4	5	116
A. thaliana	AT1G32210	_	Chr01	Block	4	5	115
	AT2G35520	+	Chr02	Block	4	5	116
Brassica rapa	BR05G20160	+	ChrA05	Block	4	5	115
	BR09G26700^a	+	ChrA09	Block	6	7	201 (88) ^d
Capsella rubella	CRU_001G29110	_	Scaffold_1	Block	4	5	115
	CRU_004G16620	+	Scaffold_4	Block	4	5	115
Citrullus lanatus	CL10G00840	+	Chr10		4	5	115
Cucumis melo	CM00021G01290	_	Scaffold00021		4	5	115
Eucalyptus grandis	EG0008G05930	+	Scaffold_8		4	5	115
Fragaria vesca	FV2G07670	+	LG2		4	5	124
Gossypium raimondii	GR03G18540	+	Chr03	Block	4	5	117
	GR08G22400	_	Chr08	Block	4	5	117
Malus domestica	MD05G025840	+	Chr05	Random	4	5	119
	MD10G000120	+	Chr10	Random	4	5	119
Manihot esculenta	ME04430G00010	+	Scaffold04430	Random	4	5	115
	ME07304G00010	+	Scaffold07304	Random	4	5	115
Populus trichocarpa	PT01G13680	_	Chr01	Block	4	5	115
	PT03G09680	+	Chr03	Block	4	5	115
Prunus persica	PPE_004G33460	_	Scaffold_4	Block	4	5	119
	PPE_008G00790	_	Scaffold_8	Block	4	5	119
Ricinus communis	RC29634G00390	+	29634	Random	4	5	115
	RC30068G01440	+	30068	Random	4	5	113
Solanum lycopersicum	SL08G076460	+	Chr08		4	5	116
S. tuberosum	ST08G008690	_	Chr08	Block	4	5	116
	ST08G021840	_	Chr08	Block	4	5	116
Thellungiella parvula	TP1G27890	_	Chr1-1		4	5	115
Theobroma cacao	TC0003G30500	+	Scaffold_3		4	5	116
Vitis vinifera	VV02G01690	+	Chr02		4	5	115
Moncot
Brachypodium distachyon	BD1G50180	+	Chr01		4	5	114
Hordeum vulgare	HV1571041G00020	_	Contig_1571041	Random	4	5	114
	HV44460G00030	+	Contig_44460	Random	4	5	114
Oryza sativa	OS04G32550	+	Chr04		4	5	114
Setaria italica	SI004G00880	+	Scaffold_4		4	5	114
Sorghum bicolor	SB10G001000	+	Chr10		4	5	114
Zea mays	ZM09G06480	_	Chr09		4	5	114
Musa acuminata	MA07G17850	_	Chr07	Block	4	5	115
	MA10G06540^b	_	Chr10	Block	-	1	48 (22)^d
	MA11G08020	+	Chr11	Block	4	5	170
Basal taxon
Amborella trichopoda	ATR_00025G00360	+	Scaffold00025		4	5	121
Gymnosperm
Taxa
Ginkgo biloba^c Gnetum montanum^c	Gene ID	Strand	Chromosome	Duplication pattern	Gene structure		Amino acid (aa)
Ginkgo biloba^c Gnetum montanum^c	Gene ID	Strand	Chromosome	Duplication pattern	Intron	Exon	Amino acid (aa)
Picea abies	GBI00024938	+	6973		-	-	123
	GMO00028447	_	GTHK-0066600		-	-	113
	PAB00021420^a	_	MA_128105	Random	5	6	162 (67)^d
P. glauca^c	PAB00041636	_	MA_42912	Random	4	5	115
	PAB00057214^b	+	MA_8328929	Random	1	2	50 (45)^d
	PGL00020840	+	PUT-39823 PUT-39823		-	-	115
P. sitchensis^c	PGL00013662	+	PUT-23726 PUT-23726		-	-	115
	PGL00010558	+	PUT-16509		-	-	115
Pinus pinaster^c	PSI00016644	+	PUT-531483		-	-	148
	PSI00008404	+	PUT-21837		-	-	115
Pi. sylvestris^c	PPI00061658	_	Unigene30039		-	-	115
	PPI00006515	_	Cotig25413		-	-	115
	PSY00006071	_	Isotig31028		-	-	115
Pi. taeda	PSY00026421	+	Isotig68699		-	-	115
	PSY00004335	+	isotig24244		-	-	115
	PTA00003657	_	Scaffold464	Random	4	5	115
Pseudotsuga menziesii ^c	PTA00022345^b	+	Scaffold214279	Random	2	3	86 (72)^d
	PTA00022344^b	+	Scaffold214279	Random	1	2	44 (44)^d
Moss Physcomitrella patens	PME00105748	+	Psme_598296871		-	-	146
Moss Physcomitrella patens	PME00105747	+	Psme_598296869		-	-	115
Alga Chlamydomonas reinhardtii	PP00045G01180	+	Scaffold_45		4	5	131
Alga Chlamydomonas reinhardtii	PP00456G00180	-	Scaffold_456		4	5	114