Whole Genome Mapping and Re-Organization of the Nuclear and Mitochondrial Genomes of Babesia microti Isolates

Emmanuel Cornillot,Richard Sutton,Peter J Krause,Sylvie Randazzo,Niseema Pachikara,Stéphane Delbecq,Choukri Ben Mamoun,Joana C Silva,Amina Dassouli,Bernard Carcy,Delphine Depoix,Aprajita Garg,Roger Frutos

doi:10.1371/journal.pone.0072657

Abstract

Babesia microti is the primary causative agent of human babesiosis, an emerging pathogen that causes a malaria-like illness with possible fatal outcome in immunocompromised patients. The genome sequence of the B. microti R1 strain was reported in 2012 and revealed a distinct evolutionary path for this pathogen relative to that of other apicomplexa. Lacking from the first genome assembly and initial molecular analyses was information about the terminal ends of each chromosome, and both the exact number of chromosomes in the nuclear genome and the organization of the mitochondrial genome remained ambiguous. We have now performed various molecular analyses to characterize the nuclear and mitochondrial genomes of the B. microti R1 and Gray strains and generated high-resolution Whole Genome maps. These analyses show that the genome of B. microti consists of four nuclear chromosomes and a linear mitochondrial genome present in four different structural types. Furthermore, Whole Genome mapping allowed resolution of the chromosomal ends, identification of areas of misassembly in the R1 genome, and genomic differences between the R1 and Gray strains, which occur primarily in the telomeric regions. These studies set the stage for a better understanding of the evolution and diversity of this important human pathogen.

Highlights

Human babesiosis is an emerging tick-transmitted infection with a worldwide distribution that may cause prolonged or fatal disease primarily in neonates, adults over 50, those who acquire the infection through blood transfusion, and those who are asplenic, suffer from malignancy or HIV infection, or are immunodeficient for other reasons [1,2]
Previous efforts to separate the chromosomes of two B. microti strains, R1 and Gray, by pulsed-field gel electrophoresis (PFGE) analyses, suggested the presence of three chromosomes: KI, KII and KIII [5]
Chromosomes purified from the R1 and Gray strains were digested with the restriction enzyme NotI and the resulting fragments were separated by PFGE prior to hybridization with a radiolabeled probe conserved in the telomeric regions of each chromosome

Summary

Introduction

Human babesiosis is an emerging tick-transmitted infection with a worldwide distribution that may cause prolonged or fatal disease primarily in neonates, adults over 50, those who acquire the infection through blood transfusion, and those who are asplenic, suffer from malignancy or HIV infection, or are immunodeficient for other reasons [1,2]. Fatality rates of 6 to 9 percent have been reported among hospitalized patients and about 20 percent among those who are immunosuppressed or experience transfusiontransmitted babesiosis [1,2,3,4]. In the past several years, molecular techniques such as polymerase chain reaction (PCR) have been used to diagnose B. microti infections. B. microti presents several challenges to molecular investigation due to the lack of a long-term in vitro culture system and, until recently, of a genome assembly. Generation of the first genome sequence has remained a primary goal in the past few years

Methods

Results

Conclusion