Evolution of the AT-rich mitochondrial DNA of the root knot nematode, Meloidogyne hapla

Abstract

Mitochondrial DNA of the root knot nematode Meloidogyne hapla was investigated for intraspecific diversity and divergence from other parthenogenetic root knot nematodes. A 1,900-bp fragment containing COII, tRNAHis, 16S rRNA, ND3 and Cyt b genes has been cloned and sequenced from one individual and an 1,188-bp region within this region was sequenced from four other Australian isolates. M. hapla mtDNA is more than 80% AT-rich, like other Meloidogyne spp. Nucleotide diversity within M. hapla is some 10-fold higher than across three other parthenogenetic species of root-knot nematode (M. arenaria, M. javanica, and M. incognita), implying an earlier origin for M. hapla. Nucleotide divergence between M. hapla and its congener M. javanica is as great as that between Ascaris suum and Caenorhabditis elegans, members of different nematode subclasses, while amino acid sequence difference between Meloidogyne is more than twice as great. This is interpreted as an AT-bias-induced acceleration of the amino acid substitution rate, over and above saturation of nucleotide divergence in the strongly AT-biased DNA, on three lines of evidence: (1) in conserved blocks in 16S rDNA congeneric Meloidogyne have no more differences than between A. suum and C. elegans; (2) the Meloidogyne lineage has more amino acid changes relative to the Ascaris/Caenorhabditis lineage with respect to four of five outgroups, the exceptional outgroup being the only species (Apis) as AT-rich as Meloidogyne; and (3) between the two Meloidogyne there are more first and second but fewer third codon position changes than between the other nematode species. M. hapla is also found to contain a 102-bp tandem repeat of at least 40 copies; a size, arrangement, and position the same as in M. javanica, but sequence comparisons did not demonstrate homology between the two repeats.