Chromosome-level genome assembly of Babesia caballi reveals diversity of multigene families among Babesia species

Abstract

Background: Babesia caballi is an intraerythrocytic parasite from the phylum Apicomplexa, capable of infecting equids and causing equine piroplasmosis. However, since there is limited genome information available on B. caballi, molecular mechanisms involved in host specificity and pathogenicity of this species have not been fully elucidated yet.

Results: Genomic DNA from a B. caballi subclone was purified and sequenced using both Illumina and Nanopore technologies. The resulting assembled sequence consisted of nine contigs with a size of 12.9 Mbp, rendering a total of 5,910 protein-coding genes. The phylogenetic tree of Apicomplexan species was reconstructed using 263 orthologous genes. We identified 481 ves1-like genes and named "ves1c". In contrast, expansion of the major facilitator superfamily (mfs) observed in closely related B. bigemina and B. ovata species was not found in B. caballi. A set of repetitive units containing an open reading frame with a size of 297 bp was also identified.

Conclusions: We present a chromosome-level genome assembly of B. caballi. Our genomic data may contribute to estimating gene expansion events involving multigene families and exploring the evolution of species from this genus.

Keywords: Babesia caballi; Comparative genomics; Equine babesiosis; Multigene expansion.

Fig. 1

Orthologous-gene-based phylogenetic analysis. The phylogenetic tree was constructed using 263 orthologous genes conserved among B. caballi, B. bovis, B. bigemina, B. ovata, B. microti, B. divergens, Babesia sp. Xinjiang, P. falciparum, and T. gondii. The arrowheads represent estimated expansion events for each gene family and the de novo emergence of repetitive sequences

Fig. 2

Characterization of ves1c genes in B. caballi. A Sequence homology cluster analysis based on sequence similarity among ves-related genes of B. caballi, B. bigemina, B. divergens, B. bovis, and Babesia sp. Xinjiang. Each node represents a protein-coding gene in the five parasites species analyzed. The edges represent similarity between nodes. B Distribution of ves1c genes in B. caballi genome. The vertical lines represent ves1c loci. The horizontal lines represent contigs and their corresponding ID. The locus of the exclusively expressed ves1c gene, BcabD6B2_18120, is highlighted in red. Telomeric repeats are indicated by arrowheads

Fig. 3

Sequence homology cluster analysis of genes with more than eight transmembrane domains in B. caballi, B. bigemina, B. divergens, B. bovis, and Babesia sp. Xinjiang. Nodes and edges represent a genes and sequence similarity between nodes, respectively

Fig. 4

Sequence homology cluster analysis of B. caballi genes. Nodes and edges represent genes and sequence similarity between nodes, respectively

Fig. 5

Schematic representation of BcRS1. The light gray boxes represent intact ORFs. The dark gray boxes represent disrupted ORFs with frameshift or truncated site. Numbers represent nucleotide positions in the contig, BcabD6B2_scf02. Nucleotide and encoded amino acids of the repetitive unit are shown at the bottom