Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104158
1-Aminocyclopropane-1-carboxylic acid oxidase (ACO)
80
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
158558
1-Aminocyclopropane-1-carboxylic acid oxidase I (ACOI)
21
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
158559
1-Aminocyclopropane-1-carboxylic acid oxidase II (ACO II)
26
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
158560
1-Aminocyclopropane-1-carboxylic acid oxidase III (ACO III)
31
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104161
1-Aminocyclopropane-1-carboxylic acid synthase (ACS)
93
GSMUA_Achr5P10790_001 is composed by GSMUA_Achr5P10790_001 and GSMUA_AchrUn_randomP25130_001
158567
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase
6
158572
60S ribosomal protein L8
3
158564
Actin
26
158630
Acyl-[acyl-carrier-protein] desaturase
7
part of GP070278 family;
Orthologous to the A. thaliana genes AT1G72330 and AT1G17290
104167
Alanine aminotransferase
3
part of GP069457 family
104189
Alcohol dehydrogenase 1
5
part of the family GP000681
158623
Aluminum induced protein with YGL and LRDR motifs
12
part of GP069884 family:
Orthologous to A. thaliana genes AT5G51690 and AT1G62960
104169
Aminotransferase ACS10/ACS12
3
corresponding to GP072019 family;
Orthologous to A. thaliana gene AT2G22250
104176
Aspartate aminotransferase
1
158611
Automatic group GP000255
22
It contains genes of the GP000060 family
104202
Auxin-induced protein 5NG4
44
158634
B12D protein
7
Curr Opin Plant Biol. 2006 Jun;9(3):331-40. Epub 2006 Apr 17. Acyltransferases in plants: a good time to be BAHD. D'Auria JC. Author information. Abstract: Acylation is a common and biochemically significant modification of plant secondary metabolites. Plant BAHD acyltransferases constitute a large family of acyl CoA-utilizing enzymes whose products include small volatile esters, modified anthocyanins, as well as constitutive defense compounds and phytoalexins. The catalytic versatility of BAHD enzymes makes it very difficult to make functional predictions from primary sequence alone. Recent advances in genome sequencing and the availability of the first crystal structure of a BAHD member are, however, providing insights into the evolution and function of these acyltransferases within the plant kingdom. PMID: 16616872 [PubMed - indexed for MEDLINE]
158535
BAHD acyltransferases
59
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104156
Constitutive triple response 1 (CTR1) proteins
18
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104160
Copper Transporter Response to ANtagonist 1 (RAN1)
17
Coproporphyrinogen III oxidase family, corresponding to GP002808 family
104143
Coproporphyrinogen III oxidase superfamily
8
158596
Cytochrome B5
11
158598
Cytochrome B5-like protein
1
Orthologous to the A. thaliana genes AT4G10040 and AT1G22840
158619
Cytochrome C
5
Included in GP000241 family
104187
Dehydrogenases
12
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104152
EIN3 BINDING F-box (EBF) proteins
31
158561
Elongation factor 1-alpha
8
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104162
Ethylene insensitive 3 (EIN3)
79
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104163
Ethylene receptors (ETR1 (ethylene response 1), ETR2 , ERS1 (ethylene response sensor 1), ERS2 and EIN4 (ethylene insensitive 4))
60
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104153
Ethylene-insensitive protein 2 (EIN2)
23
part of GP070278 family;
Orthologous to the A. thaliana genes AT1G70580 and AT1G23310
104168
Glutamate--glyoxylate aminotransferase
2
Included in GP015112 family
158520
Glutathione S-transferase TAU
28
Glycosyltransferase 61 family
158807
Glycosyltransferase 61 (GT61)
219
OG-GT61-A
158805
Glycosyltransferase 61 orthogroup A (GT61-A)
164
OG-GT61-D
158806
Glycosyltransferase 61 orthogroup D (GT61-D)
37
OG-GT61-F
158804
Glycosyltransferase 61 orthogroup F (GT61-F)
7
OG-GT61-G
158803
Glycosyltransferase 61 orthogroup G (GT61-G)
11
158592
Glycosyltransferase family 61 protein
41
Orthologous to A. thaliana genes AT3G10320, AT2G41640, AT3G57380.
158590
Glycosyltransferase family 61 protein (AT3G10320, AT2G41640, AT3G57380)
2
158591
Glycosyltransferase family 61 protein (AT3G18180, AT3G18170)
39
158589
Glycosyltransferase family 61 protein (Group H)
2
158789
GRAS
397
158744
GRAS_DELLA-1,2
28
158746
GRAS_DLT
11
158749
GRAS_HAM-I,II
36
158751
GRAS_LISCL
61
158753
GRAS_LS
15
158755
GRAS_NSP1
9
158760
GRAS_NSP2-1,2,3,Amb
25
158742
GRAS_OG-DELLA-1
19
158745
GRAS_OG-DLT
11
158747
GRAS_OG-HAM-I
10
158748
GRAS_OG-HAM-II
26
158750
GRAS_OG-LISCL
61
158752
GRAS_OG-LS
15
158754
GRAS_OG-NSP1
9
158756
GRAS_OG-NSP2-1
9
158757
GRAS_OG-NSP2-2
6
158759
GRAS_OG-NSP2-3
8
158758
GRAS_OG-NSP2-Amb
2
158761
GRAS_OG-PAT-1
21
158762
GRAS_OG-PAT-2
11
158763
GRAS_OG-PAT-3
11
158764
GRAS_OG-PAT-4
15
158766
GRAS_OG-RAD1-1
10
158767
GRAS_OG-RAD1-2
4
158769
GRAS_OG-RAM1
7
158771
GRAS_OG-SCL3
25
158775
GRAS_OG-SCL32-1
11
158776
GRAS_OG-SCL32-2
8
158773
GRAS_OG-SCL4/7
12
158778
GRAS_OG-SCLA
10
158780
GRAS_OG-SCLB
18
158782
GRAS_OG-SCR-1
12
158783
GRAS_OG-SCR-2
10
158784
GRAS_OG-SCR-3
6
158786
GRAS_OG-SHR-1
12
158787
GRAS_OG-SHR-2
9
158765
GRAS_PAT-1,2,3,4
58
158768
GRAS_RAD1-1,2
14
158770
GRAS_RAM1
7
158772
GRAS_SCL3
25
158777
GRAS_SCL32-1,2
19
158774
GRAS_SCL4/7
12
158779
GRAS_SCLA
10
158781
GRAS_SCLB
18
158788
GRAS_SHR-1,2
21
158627
Haloacid dehalogenase-like hydrolase domain-containing
4
158581
HB1/HB2 non-symbiotic hemoglobin 1/2
3
corresponding to the GP132305 family;
Orthologous to the A. thaliana genes AT5G10330 andAT1G71920
104177
Histidinol-phosphate aminotransferase
1
hydroxyacylglutathione hydrolase, GP001163 family
104139
Hydroxyacylglutathione hydrolase
5
158577
Hydroxyacylglutathione hydrolase / glyoxalase II family
5
158652
Hypoxia-responsive family
6
158638
Iron/manganese superoxide dismutase
7
part of GP071426 family;
An ortholog gene is not annoted in V. vinifera.
104175
Kynurenine-oxoglutarate transaminase
1
Orthologous to the A. thaliana gene AT1G03475
104144
LIN2 Coproporphyrinogen-III oxidase
3
corresponding to the GP070340 family;
Orthologous to the A. thaliana genes AT4G33680 and AT2G13810
104178
LL-diaminopimelate aminotransferase
2
corresponding to the GP072698 family;
Orthologous to the A. thaliana gene AT1G80360
104179
Methionine-specific aminotransferase
1
Figure 2 in the coffee genome publication: The Coffee Genome Provides Insight into the Convergent Evolution of Caffeine(2014)
158539
N-methyltransferases (NMTs)
35
Coffee genome paper 2014. Figure S29. Maximum likelihood phylogeny of known caffeine biosynthetic genes in coffee, tea, and cacao, plus 2 linked and coordinately-expressed NMTs from coffee and 7 genes with non-caffeine function from Arabidopsis.
158545
N-methyltransferases (NMTs)
19
Coffee genome paper 2014. Figure S24: Molecular phylogenetic analysis of C. canephora NMT proteins
158544
N-methyltransferases (NMTs) in Coffea
16
Coffee genome 2014. Figure S23. NMT Phylogenetic relationships of the six putative full-length NMT CDS identified in the
genome and the NMTs from C. canephoraor C. arabica
158540
N-methyltransferases (NMTs) in Coffea (from CDS)
16
NAC sequences analysed in Cenci et al. 2014
104064
NAC transcription factors
407
Orthologous to the A. thaliana genes AT2G47970 and AT3G63000
104145
NPL4-like protein-like
2
It contains genes of GP016361 family
158510
Organic cation/carnitine transporter
3
158568
Oxidoreductase, 2OG-Fe(II) oxygenase
2
Superfamily containing five Orthologous groups
158565
Oxoglutarate/iron-dependent oxygenase
15
158570
Oxoglutarate/iron-dependent oxygenase
3
Part of GP001040 family
158519
OZS1 guard cell S-type anion channel SLAC1
4
part of GP000018 family; orthologous to A. thaliana genes AT5G06720 and AT5G06730; orthologous to V. vinifera loci LOC100260291, LOC100265513 and LOC100265920
158537
Peroxidase 53/54
4
Part of GP000018 family; Orthologous to A. thaliana gene AT5G19890 qnd to V. vinifera locus LOC100253646
158536
Peroxidase 59 (AT5G19890)
3
Corresponding to Family GP000187
158618
Phosphofructokinase family
18
158566
Prolyl-4 hydroxylase
3
158649
Pyruvate kinase superfamily
23
Jourda, C., Cardi, C., Bocs, S., Garsmeur, O., D'Hont, A., & Yahiaoui, N. (2014). Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage specific whole genome duplications. New Phytologist, 202(3), 986-1000.
http://www.ncbi.nlm.nih.gov/pubmed/24716518
104154
Reversion-to-ethylene sensitivity1 (RTE1) and RTE1 homologs (RTH)
26
Included in GP001040 family
158516
S-type anion channel
14
Part of GP001040 family
158517
S-type anion channel SLAH1
5
Seed storage LTP, GP000311 family
104147
Seed storage LTP
14
Part of GP001040 family
158518
SLAH3 SLAC1 homologue 3
5
Corresponding to GP000499
158642
Thiamine pyrophosphate enzyme superfamily
9
Group orthologous to AT2G19350 and AT4G29850
158574
Transmembrane protein 230-like
4
It includes genes of GP000593
104195
Trehalose-phosphate phosphatase
19
158562
Tubulin beta-1 chain
21
part of GP070283 family; it is orthologous to the gene involved in ROOTY/SUPERROOT1 phenotype in A. thaliana;
Orthologous to the A. thaliana genes AT5G36160, AT5G53970 and AT2G20610
104181
Tyrosine aminotransferase
2
uncharacterized similar to Vitis vinifera LOC100248470;
Orthologous to the A. thaliana gene AT1G69980
104146
Unannotated cluster
3
It coreesponds to the GP000239 family
104166
Unannotated cluster
29
Orthologous to the A. thaliana gene AT5G53970
104180
Utyrosine aminotransferase
1
It includes member of GP000908 family
104199
Wound-responsive family protein
17
all sequences are included in GP000632
104123
YABBY and DROOPING LEAF
25
included in GP070758 and GP139598 families
104182
Zinc finger protein CONSTANS-LIKE
12