Dataset Information

Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution.

ABSTRACT: Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

SUBMITTER: Ying J

PROVIDER: S-EPMC6948317 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution.

Ying Jianchao J Ye Jun J Xu Teng T Wang Qian Q Bao Qiyu Q Li Aifang A

International journal of genomics 20191218

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes o ...[more]

PMID: 31950028

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Project description:IntroductionStreptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery.MethodsThree S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes.ResultsWhole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains. Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase.DiscussionIn summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.

Project description:Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites.The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp.The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms.

Dataset Information

Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution.

Publications

Comparative Genomic Analysis of <i>Rhodococcus equi</i>: An Insight into Genomic Diversity and Genome Evolution.

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