Genetic diversity and phylogeography of the global Theileria orientalis isolates inferred from MPSP gene sequences

Abstract

Background/objective

Theileria orientalis is a non-transforming Theileria species infecting cattle and water buffaloes. Several outbreaks of oriental theileriosis accompanied by considerable economic loss were documented in Asia, Australia, and New Zealand. The major piroplasm surface protein (MPSP) gene has frequently been used to molecularly characterize T. orientalis isolates worldwide. Various MPSP genotypes were detected with significant virulence variations. The present study provides the first in silico analysis for all globally published T. orientalis MPSP isolates to evaluate their phylogeny, diversity, and population structure.

Methods

All studies that tested T. orientalis isolates using PCR-MPSP protocols were systematically collected from various databases. Theileria orientalis MPSP-sequenced isolates on the GenBank were collected and the sequences were tested for their phylogenetic relatedness, genetic diversity, recombination, natural selection, and population structure using various software.

Results

The collected T. orientalis-MPSP isolates (n = 795) were clustered into 12 genotypes, including types 1 (Chitose), 2 (Ikeda), 3 (Buffeli), 4, 5, 7, 8, and N1-N5. The previously identified type 6 belonged to a separate species (Theileria sinensis). The previously identified type 9 was transferred to type 4. Two unidentified isolates from water buffaloes in India were clustered into a new suggested genotype “type N5”. Of the 12 genotypes, Ikeda (type 2) is the most virulent in cattle. However, a few clinical cases have also been linked to types 1 (Chitose) and 7. In water buffaloes, T. orientalis outbreaks have been linked to genotypes N2 and N5. Geographic mapping of various genotypes revealed the dispersal of types 1 and 3 worldwide. Overall, the 795 isolates comprised 532 haplotypes and displayed very high nucleotide (π = 0.14) and haplotype (Hd = 0.995) diversities. As a result, a very low sequence conservation value (C = 0.207) was determined. The twelve genotypes displayed comparable haplotype diversities accompanied by statistically significant negative Tajima's D and Fu's Fs values suggesting population expansion. A high value for the minimum number of recombination events (Rm = 65) was estimated for the 795 isolates, and this value varied from 0 to 23 at the genotype level. Most types also displayed significant positive selection (dn/ds ratio > 1). This suggests that both recombination and positive selection occur in T. orientalis MPSP gene, which could explain the very high genetic diversity among various T. orientalis types. Different patterns were detected for the gene flow among T. orientalis populations from various hosts and geographies; however, there is evidence for the genetic relatedness between populations from neighbouring countries.

Conclusion

The high genetic polymorphism and different associated pathogenicity in T. orientalis-MPSP genotypes highlight the need for further investigations employing whole genome sequencing technology to provide accurate comparative gene-level analyses and help further understand their pathogenicity.