Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Zhou, Huijuan; Hu, Yiheng; Ebrahimi, Aziz; Liu, Peiliang; Woeste, Keith; Zhao, Peng; Zhang, Shuoxin

doi:10.1186/s12862-021-01917-3

BMC Ecology and Evolution

Table 2 Summary of variants from all Juglandaceae genomes based on comparison with Juglans regia whole genome sequences

From: Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Species	cp-SNPs	nr-SNPs	cp-Indels	Ts/Tv ratio	Mapped %	Heterozygosity	Homozygosity	Het-ratio %
Alfaropsis roxburghiana	1959	215,357	166	1.17/1.66	55.74	10,655	204,702	4.94
Carya cathayensis	1131	253,730	288	1.04/1.43	53.16	9,006	244,724	3.54
Carya hunanensis	1066	275,372	241	1.14/1.45	84.00	21,179	254,193	7.69
Carya illinoensis	1100	761,308	268	1.05/2.28	44.90	263,845	497,463	34.65
Carya kweichwensis	1102	326,824	24	1.09/1.43	66.91	23,680	303,144	7.24
Carya sinensis	1041	344,322	5	1.01/1.56	69.18	26,548	325,860	6.88
Cyclocarya paliurus	676	483,874	9	0.77/1.43	56.99	40,571	443,303	8.38
Juglans ailantifolia	433	443,059	134	1.02/1.61	37.64	21,704	421,355	4.89
Juglans cathayensis	458	1,143,008	23	1.05/1.61	45.01	120,312	1,022,696	10.52
Juglans cinerea	482	1,014,615	109	0.99/1.64	71.72	80,304	934,311	7.91
Juglans hindsii	376	361,913	46	1.12/1.43	68.84	17,962	343,951	4.96
Juglans hopeiensis	368	990,423	26	0.83/1.82	61.78	540,892	449,531	54.61
Juglans major	472	943,553	15	0.93/1.65	84.57	73,817	869,736	7.82
Juglans mandshurica	455	1,059,545	32	0.97/1.63	92.58	110,349	9,49,196	10.41
Juglans microcarpa	374	949,180	106	1.23/1.66	98.11	111,259	837,921	11.72
Juglans regia	0	742,382	0	0.00/2.29	96.69	225,592	516,790	30.38
Juglans sigillata	6	1,051,470	2	0.20/2.29	46.02	421,420	630,050	40.07
Juglans nigra	478	682,382	3	0.94/1.66	69.12	166	1871	8.14
Platycarya strobilacea	1465	319,852	22	1.33/1.49	97.71	39,263	280,589	12.27
Pterocarya delavayi	495	686,705	123	1.09/1.43	64.74	45,839	640,866	6.67
Pterocarya fraxinifolia	506	621,411	103	1.11/1.42	23.93	37,402	584,009	6.01
Pterocarya hupehensis	505	515,964	75	1.17/1.45	36.97	35,974	479,990	6.97
Pterocarya insignis	506	589,290	116	1.00/1.43	98.45	41,877	547,413	7.10
Pterocarya macroptera	513	430,744	153	1.11/1.42	72.96	23,897	406,847	5.54
Pterocarya stenoptera	483	653,976	28	1.12/1.39	86.64	53,662	600,314	8.20
Pterocarya tonkinensis	487	547,524	133	1.05/1.44	68.29	33,764	513,760	6.16
Rhoiptelea chiliantha	2126	202,314	179	1.21/1.71	58.22	11,023	196,822	4.78

cp-SNPs the number of SNPs of chloroplast genomes, nr-SNPs the number of SNPs of whole genome resequencing, cp-Indels the number of Indels of chloroplast genomes, Ts/Tv ratio the transition/transversion ratio based on chloroplast genomes and whole genome resequencing data respectively, Mapped the mapped ratio of whole genome resequencing data used common walnut genome sequence data, Het-ratio the Heterozygosity ratio of each samples based on the whole genome resequencing data

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