物种分化因素影响下的巴尔通体差异转录组分析

doi:10.16288/j.yczz.24-201

遗传 ›› 2025, Vol. 47 ›› Issue (3): 366-381.doi: 10.16288/j.yczz.24-201

物种分化因素影响下的巴尔通体差异转录组分析

陈敏(), 韩娜, 缪玉, 强裕俊, 张雯, 刘蓬勃, 刘起勇, 栗冬梅()

中国疾病预防控制中心传染病预防控制所，传染病溯源预警与智能决策全国重点实验室，北京 102206

收稿日期:2024-07-01 修回日期:2024-09-18 出版日期:2025-03-20 发布日期:2024-09-25
通讯作者: 栗冬梅，博士，研究员，研究方向：细菌分类与进化。E-mail: lidongmei@icdc.cn
作者简介:陈敏，硕士研究生，专业方向：病原生物学。E-mail: cm593691225@163.com
基金资助:
国家自然科学基金项目(31970005);公共卫生应急反应机制的运行-传染病防控(102393220020020000029)

Differential transcriptome profiling of Bartonella spp. influenced by the species divergence factors

Min Chen(), Na Han, Yu Miao, Yujun Qiang, Wen Zhang, Pengbo Liu, Qiyong Liu, Dongmei Li()

National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China

Received:2024-07-01 Revised:2024-09-18 Published:2025-03-20 Online:2024-09-25
Supported by:
National Natural Science Foundation of China(31970005);Operation of Public Health Emergency Response Mechanisms-Infectious Disease Prevention and Control(102393220020020000029)

摘要/Abstract

摘要：

为揭示不同种和不同宿主来源的巴尔通体(Bartonella spp.)转录水平差异及其对进化关系的影响，本研究以来自4种巴尔通体种(汉赛巴尔通体、科勒巴尔通体、克氏巴尔通体和五日热巴尔通体)和3种宿主(家猫、猕猴和人)的共27株巴尔通体菌株为研究对象，利用Illumina高通量测序技术进行转录组测序，分析不同种和不同宿主来源菌株间的基因表达差异，并比较转录组与基因组水平的系统发育分析结果的异同。结果表明，不同种和不同宿主来源的巴尔通体菌株间的基因转录水平存在明显差异，并筛选到12个可能与宿主特异性识别相关的基因(virB10、bepC和virB4等)；此外，转录组核心基因(core genes)的核苷酸多态性(single nucleotide polymorphism, SNPs)位点序列的系统发育树显示菌株呈明显的物种聚集性。通过进一步分析发现，宿主因素对巴尔通体遗传分化具有一定的作用，而地理因素对巴尔通体遗传分化的作用相对较小，与基因组核心基因SNPs位点序列的系统发育分析结果一致。本研究通过差异转录组分析揭示了巴尔通体物种间的遗传分化和系统发育关系，发现不同种和不同宿主来源的菌株间存在规律性差异。这些差异与传统基因组分析结果一致，表明转录组数据可有效用于物种间的遗传分化研究。

关键词: 巴尔通体, 转录组, 物种分化, 基因组, 系统发育

Abstract:

To reveal the differences in transcript levels of Bartonella spp. from different species and hosts and their impacts on phylogenetic relationships, we focus on 27 strains from four Bartonella species (B. henselae, B. koehlerae, B. clarridgeiae and B. quintana) and three hosts (Felis catus, Homo sapiens and Macaca mulatta) to conduct the transcriptome sequencing using Illumina high-throughput sequencing technology. Gene expression differences between strains from different species and hosts are analyzed, and the results of phylogenetic analysis at the transcriptome and genome levels are compared. The results show significant differences in gene transcription between strains from different species and hosts. Twelve genes are screened, including virB10, bepC and virB4, which may facilitate host-specific recognition. Furthermore, phylogenetic analysis based on SNPs within the core genes of the transcriptome demonstrate species-specific clustering patterns among strains. Further analysis indicate that host factors influence the genetic divergence of strains, while geographic factors exert a small impact on this process. These findings are congruent with the phylogenetic analysis of SNPs in the core genes of the genome. Our study uses differential transcriptome analysis to reveal the genetic divergence and phylogenetic relationships of Bartonella species. And the observed regular differences between strains from different species and hosts are found to correspond with the results of traditional genome analysis. Thus, our results indicate the utility of transcriptome data in efficiently investigating the genetic divergence between species.

Key words: Bartonella, transcriptome, species divergence, genome, phylogeny

陈敏, 韩娜, 缪玉, 强裕俊, 张雯, 刘蓬勃, 刘起勇, 栗冬梅. 物种分化因素影响下的巴尔通体差异转录组分析[J]. 遗传, 2025, 47(3): 366-381.

Min Chen, Na Han, Yu Miao, Yujun Qiang, Wen Zhang, Pengbo Liu, Qiyong Liu, Dongmei Li. Differential transcriptome profiling of Bartonella spp. influenced by the species divergence factors[J]. Hereditas(Beijing), 2025, 47(3): 366-381.

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宿主	种	数量	地区	菌株
家猫	B. henselae	12	北京	M2BJCW、M6BJND、M1BJ、M13BJ
			山东	M68SHDLC、M45SHDLC、M7SHDLC、M20SHD
			河南	M61HENAN、M145HEN、M8HEN
			美国	Houston-1(ATCC 49882)
	B. koehlerae	1	美国	C-29(ATCC 700693)
	B. clarridgeiae	2	美国	Houston-2 cat(ATCC 51734)
	B. clarridgeiae	2	河南	M9HENGX
猕猴	B. quintana	12	四川	HOU35SC、HOU38SC、HOU40SC、HOU52SC、HOU56SC、HOU98SC、HOU11SC、HOU128SC、HOU6SC
猕猴	B. quintana	12	北京	S13、M22
人	B. quintana	1	美国	Toulose(ATCC VR-358)

宿主	种	菌株	原始读数	干净读数	干净碱基(Gb)	Q30 (%)	GC (%)
家猫	B. henselae	M1BJ	19,373,610	17,135,816	2.4	94.48	49.28
		M2BJCW	20,214,804	17,079,420	2.4	94.26	39.19
		M6BJND	25,446,512	23,753,754	3.4	93.93	42.50
		M8HEN	22,528,882	20,764,324	3.0	91.79	41.87
		M13BJ	26,843,230	17,893,966	2.6	94.04	40.79
		M20SHDLC	24,957,434	16,708,256	2.4	93.39	39.83
		M61HENAN	25,530,012	23,739,144	3.4	94.73	49.26
		M68SHDLC	19,484,726	17,703,444	2.6	93.71	41.57
		M45SHDLC	28,372,858	21,239,212	3.0	91.98	40.21
		M145HEN	26,954,782	24,001,022	3.4	92.68	43.92
		M7SHDLC	22,564,912	17,713,422	2.6	93.10	41.14
		Houston-1	25,882,948	15,769,192	2.2	93.47	40.71
	B. koehlerae	C-29	31,326,614	11,339,002	1.6	94.68	44.30
	B. clarridgeiae	Houston-2 cat	24,183,352	17,036,452	2.4	93.89	37.92
	B. clarridgeiae	M9HENGX	24,928,200	15,652,306	2.2	93.51	36.36
猕猴	B. quintana	HOU98SC	53,833,058	37,058,642	5.4	92.18	45.11
		HOU6SC	28,717,110	17,282,722	2.4	93.75	43.31
		M22	25,862,670	14,615,018	2.0	94.69	41.72
		S13	19,242,020	17,893,966	2.6	95.50	43.90
		HOU52SC	23,663,466	20,378,338	3.0	91.45	45.73
		HOU35SC	31,005,158	25,245,900	3.6	93.42	49.65
		HOU38SC	18,593,934	13,888,642	2.6	91.44	43.41
		HOU40SC	24,852,202	23,369,370	3.4	95.04	48.24
		HOU56SC	24,512,310	18,701,146	2.6	93.88	45.53
		HOU128SC	23,994,176	19,540,850	2.8	94.27	45.11
		HOU11SC	23,544,806	17,121,884	2.4	94.26	45.57
人	B. quintana	Toulose	31,136,226	12,707,986	1.9	94.68	46.34

数据库	unigenes数量	占比
Pfam	17,405	52.04% (17,405/33,444)
Swiss-prot	30,210	90.33% (30,210/33,444)
eggNOG	17,087	51.09% (17,087/33,444)
GO	26,359	78.82% (26,359/33,444)
KEGG	22,657	67.75% (22,657/334,44)

编号	途径	编号	途径
ko03016	转运核糖核酸的生物生成	ko00785	硫辛酸代谢
ko03009	核糖体生物发生	ko00564	甘油磷脂代谢
ko03010	核糖体	ko00061	脂肪酸的生物合成
ko00240	嘧啶代谢	ko03400	DNA修复和重组蛋白
ko00230	嘌呤代谢	ko00300	赖氨酸的生物合成
ko03060	蛋白质输出	ko00020	柠檬酸循环(TCA循环)
ko02048	原核生物防御系统	ko03036	染色体和相关蛋白
ko00860	卟啉代谢	ko03110	伴侣蛋白和折叠催化剂
ko03011	核糖体	ko03410	碱基切除修复
ko01007	氨基酸相关酶	ko03070	细菌分泌系统
ko01011	肽聚糖生物合成和降解蛋白	ko00220	精氨酸的生物合成
ko00190	氧化磷酸化	ko00970	氨基酰-tRNA的生物合成

宿主	种	菌株	CDS数量
宿主	种	菌株	转录组	基因组
家猫	B. henselae	M1BJ	922	1,347
		M2BJCW	1,332	1,348
		M6BJND	1,277	1,342
		M8HEN	1,295	1,347
		M13BJ	1,326	1,326
		M20SHDLC	1,326	1,326
		M61HENAN	945	1,343
		M68SHDLC	1,315	1,341
		M45SHDLC	1,327	1,327
		M145HEN	1,220	1,330
		M7SHDLC	1,316	1,329
		Houston-1	1,348	1,348
	B. koehlerae	C-29	1,201	1,202
	B. clarridgeiae	Houston-2 cat	1,132	1,132
	B. clarridgeiae	M9HENGX	1,132	1,131
猕猴	B. quintana	HOU98SC	1,107	1,107
		HOU6SC	1,107	1,107
		M22	1,107	1,107
		S13	1,097	1,107
		HOU52SC	995	1,107
		HOU35SC	813	1,109
		HOU38SC	600	1,107
		HOU40SC	923	1,107
		HOU56SC	1,107	1,107
		HOU128SC	1,107	1,107
		HOU11SC	1,107	1,107
人	B. quintana	Toulose	1,104	1,105

物种分化因素影响下的巴尔通体差异转录组分析

Differential transcriptome profiling of Bartonella spp. influenced by the species divergence factors

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组别	基因组			转录组
组别	core genes数量	accessory genes数量	cloud genes数量	core genes数量	accessory genes数量	cloud genes数量
Bh	1325	24	5	686	666	4
Bc	1131	1	0	1,130	3	0
Bq	1105	2	2	451	657	2
All	84	1,900	1,288	56	1,918	1,303

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