The objective of the present study is to determine the phylogenetic position of the Theileria organisms in blood of cattle of southern India using molecular tools. Theileria annulata (Namakkal isolate, Tamil Nadu) and three Theileria field isolates (free of T. annulata) from Wayanad, Kerala (Wayanad 1, 2, 3) were used. The small subunit ribosomal RNA (SSU rRNA) and major piroplasm surface protein (MPSP) gene products were cloned, sequenced and the phylogenetic tree constructed. SSU rRNA gene of Wayanad 1 isolate (JQ706077) revealed maximum identity with Theileria velifera or Theileria cervi. The phylogenetic tree constructed based on SSU rRNA genes revealed that Wayanad 1 isolate belonged to a new type which share common ancestor with all the other theilerial species while Wayanad 2 and 3 isolates (JX294459, JX294460) were close to types A and C respectively. Based on MPSP gene sequences, Wayanad 2 and 3 (JQ706078, JX648208) isolates belonged to Type 1 and 3 (Chitose) respectively. When, the previously reported MPSP type 7 is also considered from the same study area, Theileria orientalis types 1, 3 and 7 are observed in south India. SSU rRNA sequence of South Indian T. annulata (JX294461) showed a maximum identity with Asian isolates while the Tams1 merozoite surface antigen (MSA) gene (JX648210) showed maximum identity with north Indian isolate.
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