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Title: Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex

item Zasada, Inga
item Peetz, Amy
item HOWE, DANA - Oregon State University
item WILHELM, LARRY - Oregon State University
item CHEAM, DARAVUTH - Oregon State University
item DENVER, DEE - Oregon State University
item SMYTHE, ASHLEIGH - Hamilton College

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2014
Publication Date: 2/28/2014
Citation: Zasada, I.A., Peetz, A.B., Howe, D.K., Wilhelm, L.J., Cheam, D., Denver, D.R., Smythe, A.B. 2014. Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex. PLoS One. 9:e90035.

Interpretive Summary: Plant-parasitic nematodes are microscopic roundworms that have been shown to cause significant yield loss to a range of crops. Nematodes can cause direct damage to plants by feeding on roots but can also indirectly cause damage by transmitting plant viruses. The focus of this research was the dagger nematode which can transmit plant viruses to crops such as grapes, raspberries, and blueberries. Populations of dagger nematode were collected from across the United States from fields containing plants with or without plant virus. Each one of these populations was characterized using regions of nuclear and mitochondrial DNA. It was discovered that mitochondrial DNA may be more useful in distinguishing dagger nematode populations with the ability to transmit virus. These results are significant because they will form the basis for the development of a practical tool to distinguish virus-transmitting from non-transmitting dagger nematode populations. This research will be used by scientists and growers to better manage dagger nematode in agricultural fields.

Technical Abstract: Nematodes within the Xiphinema americanum species complex are economically important because they vector nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum is controversial, with the number of putative species being the subject of debate. Accurate phylogenetic knowledge of this group is highly desirable as it may ultimately reveal genetic differences between species which do vector nepoviruses and those which do not. For this study, X. americanum populations were collected from 12 geographically disparate locations across the U.S. from different crops and in varying association with nepoviruses. Four individuals from each population were analyzed. A portion of the 18S nuclear ribosomal DNA (rDNA) gene was sequenced for all individuals while the internal transcribed spacer region 1 (ITS1) of rDNA was cloned and 4 to 7 clones per individual were sequenced. Mitochondrial genomes for numerous individuals were sequenced in parallel using high-throughput DNA sequencing (HTS) technology. Phylogenetic analysis of the 18S rDNA revealed virtually identical sequences across all populations. Analysis of ITS1 rDNA sequences revealed several well-supported clades, with some degree of congruence with geographic location and viral transmission, but also numerous presumably paralogous sequences that failed to form clades with other sequences from the same population. Analysis of mitochondrial DNA (mtDNA) indicated the presence of three distinct monophyletic clades of X. americanum species complex nematodes. Two clades contained nematodes found in association with nepovirus and the third contained divergent mtDNA sequences from three nematode populations where nepovirus was absent. The inherent heterogeneity in ITS1 rDNA sequence data and lack of informative sites in 18S rDNA analysis suggests that mtDNA may be more useful in sorting out the taxonomic confusion of the X. americanum species complex, and might serve as an effective practical tool in distinguishing virus-vectoring from non-vectoring nematode populations.