Chorismate mutase: an alternatively spliced parasitism gene and a diagnostic marker for three important Globodera nematode species

• Published in: European journal of plant pathology Vol. 129; no. 1; pp. 89 - 102
• Main Authors: Yu, Hang, Chronis, Demosthenis, Lu, Shunwen, Wang, Xiaohong
• Format: Journal Article
• Language: English
• Published: Dordrecht Dordrecht : Springer Netherlands 2011; Springer Netherlands; Springer; Springer Nature B.V
• Subjects: Agriculture; alternative splicing; Biodiversity; Biological and medical sciences; Biomedical and Life Sciences; clones; Crop diseases; Ecology; Fundamental and applied biological sciences. Psychology; Genomes; Globodera; Globodera pallida; Globodera tabacum; intron retention; introns; Life Sciences; messenger RNA; Nematoda; Nematodes; Parasitism; Phytopathology. Animal pests. Plant and forest protection; Plant Pathology; Plant Sciences; quantitative polymerase chain reaction; regulatory sequences; Retention; root-knot nematodes; sequence analysis; TaqMan qPCR; Alternative splicing; intron retention; TaqMan qPCR; Plant pathology; Plant pathogen; Enzyme; Plant; Isomerases; Chorismate mutase; Globodera; Gene; Intron; Helmintha; Intramolecular transferases; Nemathelminthia; Invertebrata; Nematoda
• ISSN: 0929-1873; 1573-8469
• DOI: 10.1007/s10658-010-9695-9

The chorismate mutase gene is widely distributed in both cyst and root-knot nematode species and believed to play a critical role in nematode parasitism. In this study, we cloned a new chorismate mutase gene (Gt-cm-1) from Globodera tabacum and further characterized the gene structure in both G. tabacum and G. pallida, a closely related species of G. rostochiensis. The genomic clones of chorismate mutase genes from these two species were found to contain three introns with the second intron having unusual 5' and 3' splice sites. A previous study revealed that the chorismate mutase gene from G. rostochiensis is subject to alternative splicing through retention of intron 2, a process that allows for the generation of multiple mRNA transcripts from a single gene. As expected, we discovered that alternative splicing of the chorismate mutase gene is a conserved event in three Globodera species, supporting an important role of alternative splicing in regulating chorismate mutase gene function in plant parasitism by these nematodes. In addition to the potential suboptimal 5' and 3' splice sites and the small size of intron 2, detailed sequence analysis also identified candidate cis-acting elements that might be responsible for regulating intron retention of Globodera chorismate mutase genes. Based on genomic sequence variations observed, we developed TaqMan qPCR assays that provided a highly specific and sensitive identification of each Globodera species, revealing a new application of using the chorismate mutase gene as a valuable diagnostic marker for plant-parasitic nematodes.