Chinese Bulletin of Botany ›› 2017, Vol. 52 ›› Issue (5): 590-597.DOI: 10.11983/CBB16137
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Received:
2016-06-21
Accepted:
2017-01-10
Online:
2017-09-01
Published:
2017-07-10
Contact:
Ying Bao
Ying Bao, Yuqin Mei. Evolution of Defender Against Apoptotic Death (DAD) Genes in Seed Plants[J]. Chinese Bulletin of Botany, 2017, 52(5): 590-597.
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 |
Table 1 Detailed information of DAD homologous genes of 38 plants
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 |
Figure 1 Maximum likelihood tree of DAD genes based on 58 amino acid sequences of 38 plantsNumbers near branches represent bootstrap values (>50%) of the maximum likelihood analysis and posterior rate of the Bayesian analysis. The gene loci in this figure are the same as those listed in Table 1.
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