Comparative genomics analysis of Mycoplasma capricolum subsp. capricolum MOR20

Q3 Agricultural and Biological Sciences Ecological Genetics and Genomics Pub Date : 2024-07-02 DOI:10.1016/j.egg.2024.100277

Semmate Noha , Zouhair Elkarhat , Slimane Khayi , Mazen Saleh , Siham Fellahi , Ouafaa Fassi Fihri , Mehdi Elharrak

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Abstract

Mycoplasma capricolum subsp. capricolum (Mcc) is an etiological agent of Contagious Agalactia (CA) in small ruminants and belongs to Mycoplasma mycoides cluster. Until today, six strains genomes and candidates of Mcc were sequenced in Germany, USA, France and China. The aim of the present study is to analyze the genomic sequence of Mcc MOR20 strain and to compare it with the other sequenced strains. Indeed, the genome sequence of Mcc MOR20 strain was obtained using Illumina NovaSeq 6000 platform. NGS sequencing reads were assembled de novo using CLC genomics v12 (Qiagen). The variant calling on MOR20 strain was conducted using SNIPPY tools. The phylogenomic analysis of Mcc MOR20 strain was performed using BuscoPhylo pipeline. Thus, the genome of Mcc MOR20 characterized by 960,401 bp and encoded for 820 protein-coding genes, 15 rRNA genes (5S, 16S, and 23S), 34 tRNA genes, and three ncRNA genes. In addition, Mcc MOR20 is genetically closer to Mcc isolate human case with percentage of 98.58 %. In addition, the Mcc MOR20 show a genomic relationship with Mccp clade, and they share the same must of potential virulence genes that were identified, including variable surface lipoproteins and metabolic enzymes. The results of this study could be of interest for contagious agalactia vaccine development and the conserved gene might be taken as candidate for new markers for Mcc diagnosis.

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冠突支原体亚种冠突支原体 MOR20 的比较基因组学分析

冠状支原体冠状亚种（Mcc）是小反刍动物传染性无乳症（CA）的病原体，属于支原体簇。迄今为止，德国、美国、法国和中国已对六株 Mcc 的基因组和候选株进行了测序。本研究旨在分析 Mcc MOR20 菌株的基因组序列，并将其与其他已测序菌株进行比较。事实上，Mcc MOR20 菌株的基因组序列是利用 Illumina NovaSeq 6000 平台获得的。使用 CLC genomics v12 (Qiagen)对 NGS 测序读数进行了从头组装。使用 SNIPPY 工具对 MOR20 菌株进行变异调用。使用 BuscoPhylo 管道对 Mcc MOR20 菌株进行了系统进化分析。因此，Mcc MOR20 的基因组特征为 960,401 bp，编码 820 个蛋白质编码基因、15 个 rRNA 基因（5S、16S 和 23S）、34 个 tRNA 基因和 3 个 ncRNA 基因。此外，Mcc MOR20 与人类病例中分离出的 Mcc 在基因上更为接近，比例高达 98.58%。此外，Mcc MOR20 与 Mccp 支系有基因组学上的联系，它们共享已确定的潜在毒力基因，包括可变表面脂蛋白和代谢酶。这项研究的结果可能对传染性无乳症疫苗的开发有意义，而且保守基因可能被作为候选的 Mcc 诊断新标记。

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来源期刊

Ecological Genetics and Genomics Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics

CiteScore

1.80

自引率

0.00%

发文量

期刊介绍： Ecological Genetics and Genomics publishes ecological studies of broad interest that provide significant insight into ecological interactions or/ and species diversification. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are shared where appropriate. The journal also provides Reviews, and Perspectives articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context. Topics include: -metagenomics -population genetics/genomics -evolutionary ecology -conservation and molecular adaptation -speciation genetics -environmental and marine genomics -ecological simulation -genomic divergence of organisms