Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis

doi:10.12302/j.issn.1000-2006.202110030

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (1): 163-170.doi: 10.12302/j.issn.1000-2006.202110030

Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis

MA Qiuyue¹(), WANG Yuxiao², LI Qianzhong¹^,^*(), LI Shushun¹, WEN Jing¹, ZHU Lu¹, YAN Kunyuan¹, DU Yiming¹, XIE Zhijun³, LI Shuxian², OUYANG Fangqun⁴, LU Chengdai⁵

1. Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
2. Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
3. Forestry Science and Technology Spreading Station in Xiangyang, Xiangyang 441000, China
4. Beijing Botanical Garden,Beijing 100093, China
5. Institute of Acer pentaphyllum Plant Protection in Tianshui, Tianshui 741000, China

Received:2021-10-15 Accepted:2022-03-22 Online:2023-01-30 Published:2023-02-01
Contact: LI Qianzhong E-mail:yue.870808@163.com;qianzhongli@jaas.ac.cn

Abstract

Abstract:

【Objective】 There are variety species in the genus Acer, which have broad prospects for development and application in the ornamental, oil and medicinal fields. To provide an important theoretical reference for molecular biology and cytology studies of Acer, the genome sizes of six species of Acer were estimated using flow cytometry and K-mer analysis. 【Method】 Fresh leaves of six species of Acer were collected, and woody plant buffer(WPB) was used as a nuclear dissociation solution, Glycine max ‘Polanka’ and Zea mays CE-777 as internal standard. Six genome sizes were estimated by flow cytometry and K-mer analysis. 【Result】 The results of flow cytometry showed that the genomes of Acer henryi, A. buergerianum, A. elegantulum, A. griseum, A. pentaphyllum and A. tegmentosum were successfully estimated. The genome sizes of those were (691.12±8.69),(863.90±8.69), (896.50±4.35), (893.24±8.69), (766.10±8.69) and (1 154.04±13.04) Mb, respectively. The K-mer analysis showed that they were 561.72, 743.00, 777.87, 771.51, 650.64 and 1 103.46 Mb, respectively. The hybridity rate was about 1.00%、1.24%、1.31%、1.08%、0.28% and 0.81%, respectively,which were slightly smaller than that flow cytometry. 【Conclusion】 The results of this study could enrich the Acer gene database and provide important foundations for genomic and molecular cytogenetics studies within this genus.

Key words: Acer, genome size, flow cytometry, K-mer analysis

CLC Number:

S687.9
S722

MA Qiuyue, WANG Yuxiao, LI Qianzhong, LI Shushun, WEN Jing, ZHU Lu, YAN Kunyuan, DU Yiming, XIE Zhijun, LI Shuxian, OUYANG Fangqun, LU Chengdai. Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2023, 47(1): 163-170.

Figures/Tables 6

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Fig.2

Table 1

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Table 2

Table 3

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树种 species		样品峰值 peak value of samples		参照物峰值 peak value of reference		二者比值 ratio		1C值/pg 1C value		基因组大小/Mb genome size		平均值/Mb mean value
建始槭 A. henryi		9 035		16 057		0.56		0.70		684.60
		10 256		17 872		0.57		0.72		704.16		691.12±8.69
		9 210		16 358		0.56		0.70		684.60
三角枫 A. buergerianum		10 955		15 684		0.70		0.87		850.86
		12 005		16 819		0.71		0.89		870.42		863.90±8.69
		9 471		13 271		0.71		0.89		870.42
秀丽槭 A. elegantulum		9 598		13 072		0.73		0.92		899.76
		9 861		13 454		0.73		0.92		899.76		896.50±4.35
		10 468		14 347		0.73		0.91		889.98
血皮槭 A. griseum		11 489		16 032		0.72		0.90		880.2
		11 327		15 471		0.73		0.92		899.76		893.24±8.69
		11 173		15 212		0.73		0.92		899.76
五小叶槭 A. pentaphyllum	10 641		16 896		0.63		0.79		772.62
	10 570		17 174		0.62		0.77		753.06		766.10±8.69
	10 115		16 091		0.63		0.79		772.62
青楷槭 A. tegmentosum	11 688		26 393		0.44		1.20		1 173.60
	10 665		24 630		0.43		1.18		1 154.04		1 154.04±13.04
	10 768		25 291		0.43		1.16		1 134.48

树种 species	原始数据量/Gb raw data	过滤后数据量/Gb clean data	错误率/% error rate	Q20/%	Q30/%	GC含量/% GC content
建始槭 A. henryi	35.19	34.59	0.04	97.23	92.47	35.20
三角枫 A. buergerianum	35.73	34.80	0.04	97.14	92.27	34.88
秀丽槭 A. elegantulum	35.40	34.62	0.04	97.30	92.68	35.65
血皮槭 A. griseum	38.69	36.78	0.04	97.14	92.28	35.63
五小叶槭 A. pentaphyllum	35.14	34.45	0.04	97.17	92.44	35.63
青楷槭 A. tegmentosum	35.95	34.76	0.04	96.03	92.10	38.16

树种 species	K-mer 数量/Mb K-mer number	基因组大小/Mb genome size	修正后基因组大小/Mb corrected genome size	重复率/% repeat ratio	杂合率/% heterozygous ratio
建始槭 A. henryi	25 685 382 703	570.79	561.72	58.10	1.00
三角枫 A. buergerianum	25 659 241 583	754.68	743.00	63.83	1.24
秀丽槭 A. elegantulum	26 024 758 028	788.63	777.87	66.44	1.31
血皮槭 A. griseum	29 032 941 887	784.67	771.51	67.44	1.08
五小叶槭 A. pentaphyllum	25 095 510 589	660.41	650.64	63.73	0.28
青楷槭 A. tegmentosum	29 961 155 166	1 123.38	1 103.46	76.82	0.81

Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis

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