Dicots PLAZA 4.5 : Gene family expansion analysis

Gene family expansion analysis

Tool which reports the expansion/depletion of a species/lineage (through gene copy number variation compared to total proteome sizes of the species) within a gene family.

Gene family: HOM04D000133
Gene count gene family: 1389
Total coding gene count: 1,833,029
Keywords

Organisms

Organism	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Capsicum annuum	35,884	0	1.96%	0%	0
Solanum tuberosum	39,028	30	2.13%	2.16%	1.01
Solanum lycopersicum	34,725	26	1.89%	1.87%	0.99
Petunia axillaris	32,928	59	1.8%	4.25%	2.36
Erythranthe guttata	28,140	11	1.54%	0.79%	0.51
Utricularia gibba	25,930	17	1.41%	1.22%	0.87
Coffea canephora	25,574	39	1.4%	2.81%	2.01
Daucus carota	32,113	12	1.75%	0.86%	0.49
Actinidia chinensis	39,040	16	2.13%	1.15%	0.54
Amaranthus hypochondriacus	23,847	22	1.3%	1.58%	1.22
Chenopodium quinoa	44,776	40	2.44%	2.88%	1.18
Beta vulgaris	26,920	18	1.47%	1.3%	0.88
Arabidopsis lyrata	31,073	51	1.7%	3.67%	2.16
Arabidopsis thaliana	27,655	55	1.51%	3.96%	2.62
Capsella rubella	26,521	68	1.45%	4.9%	3.38
Brassica rapa	40,492	66	2.21%	4.75%	2.15
Brassica oleracea	59,220	122	3.23%	8.78%	2.72
Schrenkiella parvula	26,313	39	1.44%	2.81%	1.95
Tarenaya hassleriana	27,396	67	1.49%	4.82%	3.23
Carica papaya	27,768	15	1.51%	1.08%	0.72
Corchorus olitorius	35,704	26	1.95%	1.87%	0.96
Theobroma cacao	29,232	14	1.59%	1.01%	0.64
Gossypium raimondii	37,505	15	2.05%	1.08%	0.53
Citrus clementina	24,533	14	1.34%	1.01%	0.75
Eucalyptus grandis	36,349	29	1.98%	2.09%	1.06
Malus domestica	53,922	22	2.94%	1.58%	0.54
Pyrus bretschneideri	42,812	17	2.34%	1.22%	0.52
Prunus persica	26,873	11	1.47%	0.79%	0.54
Fragaria vesca	32,831	9	1.79%	0.65%	0.36
Ziziphus jujuba	29,293	13	1.6%	0.94%	0.59
Cucumis melo	27,427	10	1.5%	0.72%	0.48
Cucumis sativus L.	21,503	12	1.17%	0.86%	0.74
Citrullus lanatus	23,440	14	1.28%	1.01%	0.79
Medicago truncatula	50,894	52	2.78%	3.74%	1.35
Trifolium pratense	39,948	67	2.18%	4.82%	2.21
Cicer arietinum	23,550	31	1.28%	2.23%	1.74
Cajanus cajan	48,680	21	2.66%	1.51%	0.57
Glycine max	56,044	27	3.06%	1.94%	0.63
Vigna radiata var. radiata	22,368	16	1.22%	1.15%	0.94
Arachis ipaensis	41,840	11	2.28%	0.79%	0.35
Hevea brasiliensis	35,196	8	1.92%	0.58%	0.3
Manihot esculenta	33,033	13	1.8%	0.94%	0.52
Ricinus communis	31,221	9	1.7%	0.65%	0.38
Populus trichocarpa	42,950	15	2.34%	1.08%	0.46
Vitis vinifera	26,346	23	1.44%	1.66%	1.15
Nelumbo nucifera	26,685	8	1.46%	0.58%	0.4
Oryza sativa ssp. japonica	42,189	39	2.3%	2.81%	1.22
Zea mays	39,498	17	2.15%	1.22%	0.57
Amborella trichopoda	26,846	19	1.46%	1.37%	0.94
Picea abies	66,632	9	3.64%	0.65%	0.18
Selaginella moellendorffii	22,285	14	1.22%	1.01%	0.83
Marchantia polymorpha	19,287	2	1.05%	0.14%	0.13
Physcomitrium patens	32,926	9	1.8%	0.65%	0.36
Chlamydomonas reinhardtii	17,741	0	0.97%	0%	0
Micromonas commoda	10,103	0	0.55%	0%	0

Phylogenetic clades

Clade	Num species	Total genes	Genes in family	Percentage total	Percentage family	Ratio family vs. total
Solanum	2	73,753	56	4.02%	4.03%	1
Solanoideae	3	109,637	56	5.98%	4.03%	0.67
Solanaceae	4	142,565	115	7.78%	8.28%	1.06
Lamiales	2	54,070	28	2.95%	2.02%	0.68
Lamiids	7	222,209	182	12.12%	13.1%	1.08
Asterids	9	293,362	210	16%	15.12%	0.95
Chenopodiaceae	2	71,696	58	3.91%	4.18%	1.07
Caryophyllales	3	95,543	80	5.21%	5.76%	1.11
Arabidopsis	2	58,728	106	3.2%	7.63%	2.38
Camelineae	3	85,249	174	4.65%	12.53%	2.69
Brassica	2	99,712	188	5.44%	13.53%	2.49
Brassicaceae	6	211,274	401	11.53%	28.87%	2.5
Brassicales	8	266,438	483	14.54%	34.77%	2.39
Malvaceae	3	102,441	55	5.59%	3.96%	0.71
Malvids	13	429,761	581	23.45%	41.83%	1.78
Maleae	2	96,734	39	5.28%	2.81%	0.53
Maloideae	3	123,607	50	6.74%	3.6%	0.53
Rosaceae	4	156,438	59	8.53%	4.25%	0.5
Rosales	5	185,731	72	10.13%	5.18%	0.51
Cucumis	2	48,930	22	2.67%	1.58%	0.59
Benincaseae	3	72,370	36	3.95%	2.59%	0.66
Trifolieae	2	90,842	119	4.96%	8.57%	1.73
Phaseoleae	3	127,092	64	6.93%	4.61%	0.67
Papilionoideae	7	283,324	225	15.46%	16.2%	1.05
Crotonoideae	2	68,229	21	3.72%	1.51%	0.41
Euphorbiaceae	3	99,450	30	5.43%	2.16%	0.4
Malpighiales	4	142,400	45	7.77%	3.24%	0.42
Fabids	19	683,825	378	37.31%	27.21%	0.73
Rosids	33	1,139,932	982	62.19%	70.7%	1.14
Pentapetalae	45	1,528,837	1,272	83.4%	91.58%	1.1
Eudicotyledons	46	1,555,522	1,280	84.86%	92.15%	1.09
Poaceae	2	81,687	56	4.46%	4.03%	0.9
Mesangiospermae	48	1,637,209	1,336	89.32%	96.18%	1.08
Magnoliophyta	49	1,664,055	1,355	90.78%	97.55%	1.07
Spermatophyta	50	1,730,687	1,364	94.42%	98.2%	1.04
Tracheophyta	51	1,752,972	1,378	95.63%	99.21%	1.04
Embryophyta	53	1,805,185	1,389	98.48%	100%	1.02
Chlorophyta	2	27,844	0	1.52%	0%	0
Viridiplantae	55	1,833,029	1,389	100%	100%	1