植物学报 ›› 2017, Vol. 52 ›› Issue (5): 590-597.doi: 10.11983/CBB16137

• 研究报告 • 上一篇    下一篇

种子植物抗细胞凋亡DAD基因的演化

包颖*(), 梅玉芹   

  1. 曲阜师范大学生命科学学院, 曲阜 273165
  • 收稿日期:2016-06-21 接受日期:2017-01-10 出版日期:2017-09-01 发布日期:2017-07-10
  • 通讯作者: 包颖 E-mail:baoyingus@126.com
  • 基金资助:
    国家自然科学基金(No.31570218)

Evolution of Defender Against Apoptotic Death (DAD) Genes in Seed Plants

Ying Bao*(), Yuqin Mei   

  1. School of Life Sciences, Qufu Normal University, Qufu 273165, China
  • Received:2016-06-21 Accepted:2017-01-10 Online:2017-09-01 Published:2017-07-10
  • Contact: Ying Bao E-mail:baoyingus@126.com

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

表1

38种植物DAD同源基因的详细信息"

Taxa Gene ID Strand Chromosome Duplication
pattern
Gene structure Amino acid (aa)
Intron Exon
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
BR09G26700a + 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
MA10G06540b _ 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 bilobac
Gnetum montanumc
Gene ID Strand Chromosome Duplication
pattern
Gene structure Amino acid (aa)
Intron Exon
Picea abies GBI00024938 + 6973 - - 123
GMO00028447 _ GTHK-0066600 - - 113
PAB00021420a _ MA_128105 Random 5 6 162 (67) d
P. glaucac PAB00041636 _ MA_42912 Random 4 5 115
PAB00057214b + MA_8328929 Random 1 2 50 (45) d
PGL00020840 + PUT-39823
PUT-39823
- - 115
P. sitchensisc PGL00013662 + PUT-23726
PUT-23726
- - 115
PGL00010558 + PUT-16509 - - 115
Pinus pinasterc PSI00016644 + PUT-531483 - - 148
PSI00008404 + PUT-21837 - - 115
Pi. sylvestrisc 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 PTA00022345b + Scaffold214279 Random 2 3 86 (72) d
PTA00022344b + Scaffold214279 Random 1 2 44 (44) d
Moss
Physcomitrella patens
PME00105748 + Psme_598296871 - - 146
PME00105747 + Psme_598296869 - - 115
Alga
Chlamydomonas reinhardtii
PP00045G01180 + Scaffold_45 4 5 131
PP00456G00180 - Scaffold_456 4 5 114

图1

基于38种植物的58条DAD基因的编码序列构建的最大似然性系统发育关系树分支附近的数值分别代表最大似然性分析中大于50%的自展支持率和贝叶斯分析中的后验率, 各基因位点同表1。"

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