敬钊缨毛蛛染色体核型和基因组特征分析

doi:10.16288/j.yczz.25-026

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Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (12): 1351-1364.doi: 10.16288/j.yczz.25-026

• Research Article • Previous Articles Next Articles

Karyotype and genome characterization analysis of Chilobrachys jingzhao (Theraphosidae: Chilobrachys)

Yuxuan Zhang¹^,²(), Mengying Zhang³, Hanting Yang¹^,², Chi Song¹^,²(), Zizhong Yang³(), Shilin Chen¹^,²()

1. School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
2. Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
3. Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, College of Pharmacy, Dali University, Dali 671000, China

Received:2025-01-21 Revised:2025-03-23 Online:2025-05-21 Published:2025-05-21
Contact: Chi Song, Zizhong Yang, Shilin Chen E-mail:18744989564@163.com;songchi@cdutcm.edu.cn;yangzzh69@163.com;slchen@cdutcm.edu.cn
Supported by:
Chengdu University of Traditional Chinese Medicine Talent Introduction Research Startup Fund(030040015);Chengdu University of Traditional Chinese Medicine Talent Introduction Research Startup Fund(030040017)

Abstract

Abstract:

The medicinal preparation of Chilobrachys jingzhao possesses various therapeutic properties, including anti-inflammatory, detoxifying, analgesic, and anti-edema effects. However, research on its genetic background and toxin mechanisms is held back by the lack of chromosome karyotype and genome data. In this study, we analyzed the karyotype of C. jingzhao using chromosome preparation techniques, estimated the genome size using flow cytometry and K-mer analysis, and performed genome sequencing and assembly using second- and third-generation single molecule real-time sequencing technologies. The results showed that C. jingzhao has a diploid chromosome number of 2n=68, with a karyotype formula of 2n=46m+18sm+4st and a chromosomal complement of 2n=10L+18M2+38M1+2S. Using Solanum lycopersicum and Trichonephila clavata as references, flow cytometry estimates the genome size at 7,775.49 Mb and 7,680.26 Mb, respectively. The 19-mer analysis also estimated the genome size to be 7,626.00 Mb, consistent with the flow cytometry results. Further analysis indicated that the genome of C. jingzhao has a high level of heterozygosity (8.45%) and a high proportion of repetitive sequences (67.10%), classifying it as an ultra-high heterozygous and high-repeat genome. The initial genome assembly of C. jingzhao was 8,804.93 Mb in size, with a contig N50 of 55.55 Mb and a BUSCO completeness score of 95.9%, indicating high assembly quality. This study first reveals the karyotype and genome information of C. jingzhao, offering crucial data for future research on its whole genome, toxin mechanisms, genetics, origin, evolution, and taxonomy.

Key words: Chilobrachys jingzhao, chromosome karyotype, genome size, single molecule real-time sequencing

Yuxuan Zhang, Mengying Zhang, Hanting Yang, Chi Song, Zizhong Yang, Shilin Chen. Karyotype and genome characterization analysis of Chilobrachys jingzhao (Theraphosidae: Chilobrachys)[J]. Hereditas(Beijing), 2025, 47(12): 1351-1364.

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编号	染色体相对长度(%)±标准差	臂比±标准差	相对长度系数	染色体类型
编号	染色体相对长度(%)±标准差	臂比±标准差	相对长度系数	Levan分类标准	Kuo分类标准
1	4.59±0.14	1.17±0.02	1.56	m	L
2	4.17±0.16	1.52±0.02	1.41	m	L
3	3.91±0.05	1.35±0.03	1.33	m	L
4	3.77±0.03	1.56±0.02	1.33	m	L
5	3.62±0.02	1.24±0.04	1.28	m	L
6	3.54±0.05	1.38±0.02	1.23	m	M2
7	3.46±0.02	1.13±0.02	1.20	m	M2
8	3.43±0.02	1.44±0.02	1.17	m	M2
9	3.24±0.03	1.18±0.01	1.16	m	M2
10	3.07±0.04	1.48±0.03	1.10	m	M2
11	3.04±0.03	1.38±0.02	1.04	m	M2
12	3.04±0.03	1.44±0.02	1.03	m	M2
13	3.01±0.03	1.18±0.01	1.03	m	M2
14	2.91±0.03	1.47±0.02	1.02	m	M2
15	2.88±0.03	1.68±0.03	0.99	m	M1
16	2.78±0.03	1.23±0.01	0.98	m	M1
17	2.78±0.03	1.29±0.01	0.97	m	M1
18	2.63±0.03	1.37±0.02	0.94	m	M1
19	2.59±0.03	1.41±0.03	0.94	m	M1
20	2.52±0.03	1.43±0.01	0.93	m	M1
21	2.46±0.03	1.43±0.02	0.89	m	M1
22	2.30±0.02	1.64±0.02	0.88	m	M1
23	2.09±0.02	1.49±0.02	0.88	m	M1
24	3.91±0.04	2.74±0.02	0.86	sm	M1
25	2.85±0.03	1.74±0.02	0.83	sm	M1
26	2.74±0.03	2.34±0.04	0.83	sm	M1
27	2.59±0.03	2.97±0.03	0.80	sm	M1
28	2.37±0.03	1.85±0.02	0.80	sm	M1
29	2.37±0.03	1.84±0.02	0.79	sm	M1
30	2.33±0.02	1.79±0.02	0.78	sm	M1
31	2.30±0.02	2.50±0.03	0.78	sm	M1
32	2.23±0.02	2.02±0.03	0.76	sm	M1
33	2.46±0.03	3.77±0.06	0.76	st	M1
34	2.23±0.02	3.94±0.12	0.71	st	S

类别	总读数	总碱基数(bp)	GC含量(%)	Q20(%)	Q30(%)
原始数据	2,671,194,894	400,679,234,100	45.37	97.79	93.20
有效数据	2,671,194,792	387,721,350,746	45.13	97.80	93.18

物种	2n	性染色体系统	核型公式	参考文献
Acanthoscurria gomesiana	43~46		m, sm, st, t	[41]
Aphonopelma hentzi	44	X₁X₂O		[42]
Avicularia minatrix	78	X₁X₂X₃X₄O	52m/sm+4st+18t+X₁sm+X₂m+X₃m+X₄t	[43]
Chaetopelma olivaceum	(16)			[19]
Grammostola rosea	72	X₁X₂O	64m+4sm+2st+X₁m+X₂sm	[44]
Grammostola aff. rosea	72	X₁X₂O+2CSCP	X₁m+X₂t+CSCP1m+CSCP2sm	[45]
Holothele cf. longipes	73	X₁X₂X₃O	66m/sm+4t/T+X₁X₂X₃m/sm	[44]
Idiothele mira	25	XO	18m+2sm+2st+2t+Xm	[44]
Ischnocolus jickelii	85	X₁X₂X₃O	70m+12sm+X₁X₂X₃m/sm	[44]
Pelinobius muticus	67	X₁X₂X₃O	46t+18m/sm+X1m+X₂st+X₃t	[44]
Poecilotheria formosa	110	X₁X₂X₃X₄O	30m+18sm+18st+40t+X₁X₂X₃m+X₄sm	[20]
Psalmopoeus cambridgei	84	X₁X₂O	64m/sm+18t+X₁X₂m	[44]
Pterinochilus lugardi	23	XO+CSCP	sm, m	[45]
Pterinochilus murinus	43	XO	36m+6sm+Xm	[44]
Pterinopelma roseum	48		st, t	[41]
Tekoapora wacketi	48		st, t	[41]
Tliltocatl albopilosus	74	X₁X₂X₃X₄O	64m/sm+6st+X₁X₂X₃X₄m	[44]
Vitalius dubius	74~81		m, sm, st, t	[41]
Vitalius sorocabae	48		st, t	[41]
Vitalius sp.	48		m, sm, st, t	[41]

Karyotype and genome characterization analysis of Chilobrachys jingzhao (Theraphosidae: Chilobrachys)

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