The variations of ribosomal ITS genes in Rotylenchulus reniformis in Japan, and phylogenetic analysis of its reproductive types based on the mitochondrial COI gene

Abstract

Rotylenchulus reniformis is a parasitic nematode that causes damage to a wide range of crops worldwide. Whereas amphimictic type reniform populations are commonly found globally, the parthenogenetic type has so far been found only in Japan with no reported damage to crops. We are interested in elucidating the relationships between the amphimictic and parthenogenic types as well as their respective pathogenicity. By using the internal transcribed spacer (ITS) of ribosomal sequences and the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene, we aimed to characterize the two R. reniformis reproductive types in Japan, to examine the relationship between these two types, and to obtain information necessary for elucidating their pathogenicity. Both long and short rDNA ITS sequences from individual nematodes were obtained by PCR amplification and analyzed. Even within an individual, the long ITS sequences had considerably more variations than the short ITS. Phylogenetic analysis based on the ITS region revealed that each reproductive type formed a cluster in the clade for the long and short ITS sequences, respectively, except for two long ITS sequences, which were found in both reproductive types. The two long ITS sequences formed a cluster with the short ITS and seemed to be the intermediate of long and short ITS. Analyses of the mtDNA COI gene suggest that the two reproductive types of R. reniformis in Japan are within the intraspecific variation.