Both mechanism and age of duplications contribute to biased gene retention patterns in plants

Rody, Hugo V. S.; Baute, Gregory J.; Rieseberg, Loren H.; Oliveira, Luiz O.

doi:10.1186/s12864-016-3423-6

BMC Genomics

Table 1 Distribution of paralogous gene pairs for 25 plant species targeted by this study

From: Both mechanism and age of duplications contribute to biased gene retention patterns in plants

Specie	Chr	Initial PCG	Duplicates	Number of duplicates by duplication type			Number of duplicates by Ks range
Specie	Chr	Initial PCG	Duplicates	WGD	Tandem	Undefined	0 < Ks ≤ 0.5	0.5 < Ks ≤ 1	1 < Ks ≤ 1.5	1.5 < Ks ≤ 2	Ks > 2
Arabidopsis lyrata	16	32670	6378	3442	1816	1120	2251	2216	966	945	228
Arabidopsis thaliana	10	33602	6194	2740	1232	2222	1657	2407	1183	947	222
Amborella trichopoda	26	26460	3322	15	998	2309	1861	427	402	632	137
Brachypodium distachyon	10	26678	3573	1025	1768	780	981	1024	835	733	175
Carica papaya	18	28072	1915	24	455	1436	603	210	402	700	126
Citrullus lanatus	22	23438	2806	385	1015	1406	691	435	751	930	227
Eucalyptus grandis	22	36449	11120	390	6424	4306	8106	925	1029	1060	240
Fragaria vesca	14	34809	3974	1021	1606	1347	1500	979	684	811	184
Glycine max	40	46509	15242	9721	2087	3434	11697	1961	790	794	185
Helianthus annuus	34	44144	9925	57	995	8873	4651	2805	1551	918	108
Lotus japonicus	12	26818	2682	184	627	1871	1159	774	415	334	51
Malus domestica	34	63515	15551	2761	1308	11482	13084	1258	683	526	107
Manihot esculenta	36	30800	7134	2530	703	3901	4915	837	716	666	110
Medicago truncatula	16	57587	5098	1083	2419	1596	2902	1262	543	391	115
Oryza sativa ssp. indica	24	48788	8349	1957	2869	3523	3361	2169	1665	1154	317
Oryza sativa ssp. japonica	24	59430	5559	1482	2173	1904	1928	1584	1233	814	183
Physcomitrella patens	54	36137	3769	306	202	3261	637	1848	883	401	99
Populus trichocarpa	36	41521	9721	5609	1988	2124	7572	738	704	707	147
Ricinus communis	20	31221	2558	155	614	1789	628	435	683	812	176
Sorghum bicolor	20	34686	4267	1048	1698	1521	1468	1061	993	745	186
Solanum lycopersicum	24	34432	7100	1234	2561	3305	3184	2287	872	757	209
Selaginella moellendorffii	16–27	22285	1885	351	608	926	1457	129	102	197	66
Theobroma cacao	20	46269	3488	722	1553	1213	1199	601	822	866	201
Vitis vinifera	38	26644	4536	528	1935	2073	1918	852	1042	724	128
Zea mays	20	39597	6336	590	1396	4350	3792	1095	813	636	153

Chr Number of Chromosomes, Initial PCG Initial number of Protein-coding gene sequences

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ISSN: 1471-2164

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