鹅源副鸡禽杆菌全基因组重测序及比较基因组学分析

doi:10.11843/j.issn.0366-6964.2024.03.032

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (3): 1208-1216.doi: 10.11843/j.issn.0366-6964.2024.03.032

鹅源副鸡禽杆菌全基因组重测序及比较基因组学分析

苏文楠¹, 刘佳琪¹, 钟嘉诚¹, 陈济铛¹, 朱婉君², 张溢珊², 张济培^1,2*

1. 佛山科学技术学院, 佛山 528225;
2. 佛山天牧生物科技有限公司, 佛山 528225

收稿日期:2023-06-13 出版日期:2024-03-23 发布日期:2024-03-27
通讯作者: 张济培,主要从事水禽疾病防控研究,E-mail:fszh128@163.com
作者简介:苏文楠(1997-),男,广东肇庆人,硕士生,主要从事水禽疾病防控研究,E-mail:1193958581@qq.com
基金资助:
广东省普通高校科研项目重点领域专项（2020ZDZX1018）；横向课题（BKH20905901）

Complete Genome Re-sequence and Comparative Genomic Analysis of Avibacterium paragallinarum from Geese

SU Wennan¹, LIU Jiaqi¹, ZHONG Jiacheng¹, CHEN Jidang¹, ZHU Wanjun², ZHANG Yishan², ZHANG Jipei^1,2*

1. Foshan University of Science and Technology, Foshan 528225, China;
2. Foshan Tianmu Biotechnology Co. LTD, Foshan 528225, China

Received:2023-06-13 Online:2024-03-23 Published:2024-03-27

摘要/Abstract

摘要： 为了分析鹅源副鸡禽杆菌（Apg）与鸡源菌株的基因组差异，对3株鹅源Apg和4株鸡源Apg进行全基因重测序及基因组分析。全基因重测序结果显示7株菌株基因组片段大小为2.567 832~2.607 127 Mb，GC含量介于40.80%~40.93% 之间。SNPs同源性分析结果显示，3株鹅源菌株和鸡源C-AP3株聚集在p4chr1株的小分支上，另外3株鸡源菌株分布在其它国内菌株分支上。基因同源性分析结果显示鹅源菌株特有基因76个，鸡源菌株特有基因37个。对鹅适应性基因的筛查共聚类出79个基因，其中编码已知蛋白的基因有22个，其余编码假定蛋白；对鸡适应性基因的筛查聚类出39个基因，其中10个编码已知蛋白，29个编码假定基因。通过比较基因组学发现与Apg宿主适应性有关的基因为118个，为进一步阐释Apg跨物种感染的分子生物学机制奠定了基础。

关键词: 副鸡禽杆菌, 比较基因组学, 全基因重测序, 跨物种传播

Abstract: The aim of this paper was to analyze the differences between the genome of Avibacterium paragallinella (Apg) of goose origin and chicken. In this study, three goose Apg and four chicken Apg isolates were sequenced and their genomic components were analyzed. The results of whole gene re-sequence showed that the genome fragment size of 7 isolates was 2.567 832-2.607 127 Mb, and the GC content was between 40.80% and 40.93%. The results of SNPs homology analysis showed that three strains isolated from geese and three strains of C-AP3 from chicken were clustered on the small branch of p4chr1 strain, and the other three strains from chicken were distributed on the branches of other domestic strains. In the gene homology analysis experiment, there are 76 specific genes of goose isolate and 37 specific genes of chicken isolate. The screening results of adaptive genes in geese showed that 79 genes were co-clustered, including 22 genes encoding known proteins, and the rest encoding putative proteins. In the screening test of chicken adaptive genes, 39 genes were clustered, including 10 encoding known proteins and 29 encoding putative genes. Through comparative genomics, found 118 genes related to Apg host adaptation, which laid a foundation for further elucidation of the molecular biological mechanism of Apg cross-species infection.

Key words: Avibacterium paragallinarum, comparative genomics, whole gene resequencing, cross-species transmission

中图分类号:

S852.612

苏文楠, 刘佳琪, 钟嘉诚, 陈济铛, 朱婉君, 张溢珊, 张济培. 鹅源副鸡禽杆菌全基因组重测序及比较基因组学分析[J]. 畜牧兽医学报, 2024, 55(3): 1208-1216.

SU Wennan, LIU Jiaqi, ZHONG Jiacheng, CHEN Jidang, ZHU Wanjun, ZHANG Yishan, ZHANG Jipei. Complete Genome Re-sequence and Comparative Genomic Analysis of Avibacterium paragallinarum from Geese[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 1208-1216.

参考文献

[1] 孙惠玲, 张培君, 陈小玲, 等. 鸡传染性鼻炎研究进展[J]. 中国家禽, 2012, 34(19):42-44.
SUN H L, ZHANG P J, CHEN X L, et al. Research progress of infectious rhinitis in chickens[J]. China Poultry, 2012, 34(19):42-44. (in Chinese)
[2] REECE R L, BARR D A, OWEN A C. The isolation of Haemophilus paragallinarum from Japanese quail[J]. Aust Vet J, 1981, 57(7):350-351.
[3] WAHYUNI A E T H, TABBU C R, ARTANTO S, et al. Isolation, identification, and serotyping of Avibacterium paragallinarum from quails in Indonesia with typical infectious coryza disease symptoms[J]. Vet World, 2018, 11(4):519-524.
[4] BALOURIA A, DESHMUKH S, BANGA H S, et al. Early migration pattern of Avibacterium paragallinarum in the nasal passage of experimentally infected chicken and Japanese quail by immunohistochemistry[J]. Avian Pathol, 2019, 48(2):168-177.
[5] 支岩, 梅晨, 刘珍邑, 等. 副鸡禽杆菌毒力因子研究进展[J]. 畜牧兽医学报, 2023, 54(12):4934-4942.
ZHI Y, MEI C, LIU Z Y, et al. Research progress on the virulence factors of Avibacterium paragallinarum[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12):4934-4942.(in Chinese)
[6] 钟嘉诚, 陈济铛, 仇桂玲, 等. 鹅源副鸡禽杆菌的分离鉴定及致病性试验[J]. 中国家禽, 2021, 43(3):112-117.
ZHONG J C, CHEN J D, QIU G L, et al. Isolation, identification and pathogenicity test of AN Avibacterium paragallinarum from Goose[J]. China Poultry, 2021, 43(3):112-117. (in Chinese)
[7] 卢玉葵, 刘佳琪, 苏文楠, 等. 不同禽源副鸡禽杆菌的人工交叉致病试验[J/OL]. 中国家禽, 2023:1-7. (2023-05-19). http://kns.cnki.net/kcms/detail/32.1222.S.20230517.1717.012.html.
LU Y K, LIU J Q, SU W N, et al. Artificial cross pathogenicity test of avian Bacillus paragallinarum from goose and chicken[J/OL]. China Poultry, 2023:1-7. (2023-05-19). http://kns.cnki.net/kcms/detail/32.1222.S.20230517.1717.012.html. (in Chinese)
[8] LUO R B, LIU B H, XIE Y L, et al. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler[J]. GigaScience, 2012, 1(1):18.
[9] SEEMANN T. Prokka:rapid prokaryotic genome annotation[J]. Bioinformatics, 2014, 30(14):2068-2069.
[10] ARNDT D, GRANT J R, MARCU A, et al. PHASTER:a better, faster version of the PHAST phage search tool[J]. Nucleic Acids Res, 2016, 44(W1):W16-W21.
[11] ALTSCHUL S F, MADDEN T L, SCHÄFFER A A, et al. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Res, 1997, 25(17):3389-3402.
[12] EMMS D M, KELLY S. OrthoFinder:phylogenetic orthology inference for comparative genomics[J]. Genome Biol, 2019, 20(1):238.
[13] LIU B, POP M. ARDB-antibiotic resistance genes database[J]. Nucleic Acids Res, 2009, 37(S1):D443-D447.
[14] GUO M J, LIU D H, CHEN X F, et al. Pathogenicity and innate response to Avibacterium paragallinarum in chickens[J]. Poult Sci, 2022, 101(1):101523.
[15] LIU B, ZHENG D D, JIN Q, et al. VFDB 2019:a comparative pathogenomic platform with an interactive web interface[J]. Nucleic Acids Res, 2019, 47(D1):D687-D692.
[16] HUO C Y, ZENG X M, XU F Z, et al. The Transcriptomic and Bioinformatic characterizations of iron acquisition and Heme utilization in Avibacterium paragallinarum in response to iron-starvation[J]. Front Microbiol, 2021, 12:610196.
[17] 郭瑞亮, 张刚, 崔钦娜, 等. 细菌中基因组岛的转移与调控机制研究进展[J]. 微生物学通报, 2018, 45(10):2234-2242.
GUO R L, ZHANG G, CUI Q N, et al. Regulation, excision and horizontal transfer of genomic islands in bacteria[J]. Microbiology China, 2018, 45(10):2234-2242. (in Chinese)
[18] 迟文静, 刘宜昕, 王粟, 等. 进化树在细菌亲缘关系分析中的应用研究[J]. 检验医学, 2020, 35(12):1310-1314.
CHI W J, LIU Y X, WANG S, et al. Evolutionary tree and its application in the analysis of bacterial kinship[J]. Laboratory Medicine, 2020, 35(12):1310-1314. (in Chinese)
[19] TANG M S, WANG T, ZHANG X F. A review of SNP heritability estimation methods[J]. Brief Bioinform, 2022, 23(3):bbac067.
[20] MOHANRAO M D, SENTHILVEL S, REDDY Y R, et al. Amplifluor-based SNP genotyping[M]//SHAVRUKOV Y. Plant Genotyping:Methods and Protocols. New York:Humana, 2023:191-200.
[21] KHASSANOVA G, KHALBAYEVA S, SERIKBAY D, et al. SNP genotyping with amplifluor-like method[M]//SHAVRUKOV Y. Plant Genotyping:Methods and Protocols. New York:Humana. 2023:201-219.

鹅源副鸡禽杆菌全基因组重测序及比较基因组学分析

Complete Genome Re-sequence and Comparative Genomic Analysis of Avibacterium paragallinarum from Geese

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 3

编辑推荐

Metrics

本文评价

[1]	支岩, 梅晨, 刘珍邑, 乌云格日乐, 王宏俊, 胡格. 副鸡禽杆菌毒力因子研究进展[J]. 畜牧兽医学报, 2023, 54(12): 4934-4942.
[2]	龚建森, 徐敬潇, 付立霞, 张笛, 董永毅, 徐步, 窦新红. 印第安纳沙门菌环介导等温扩增检测方法的建立[J]. 畜牧兽医学报, 2021, 52(2): 560-564.
[3]	唐丽昕, 王天骄, 刘华淼, 张然然, 邢秀梅. 梅花鹿与欧洲马鹿染色体水平基因组的比较研究[J]. 畜牧兽医学报, 2021, 52(2): 376-388.