Meloidogyne chitwoodi is one of the most devastating pests of potato in the U.S. Pacific Northwest (PNW). Nematode-infected tubers develop external as well as internal defects, making the potatoes unmarketable, and resulting in economic losses. Draft genome assemblies of three M. chitwoodi genotypes, Mc1, Mc2 and Mc1Roza, were generated using Illumina and PacBio Sequel RS II sequencing. The final assemblies consist of 30, 39 and 38 polished contigs for Mc1, Mc2 and Mc1Roza, respectively, with average N50 of 2.37 Mb and average assembled genome size of ~47.41 Mb. An average of 10,508 genes were annotated for each genome. BUSCO analysis indicated that 69.80% of the BUSCOs were complete whereas 68.80%, 0.93% and 12.67% were single copy, duplicated and fragmented, respectively. These highly contiguous genomes will enrich resources to study potato-nematode interactions and enhance breeding efforts to develop nematode resistant potato varieties for PNW.
Columbia root-knot nematode, Meloidogyne chitwoodi, parasitizes potato plants and causes visible small brown dots in the tuber flesh that dramatically reduce the market value of the crop. In the Pacific Northwest (PNW), two races of M. chitwoodi, Race 1 and Race 2 and a pathotype Race 1Roza exist. The races and pathotype of M. chitwoodi are primarily differentiated based on host tests. Currently, M. chitwoodi can be differentiated from M. hapla or other Meloidogyne Sp. based on morphology and by molecular markers however, the different pathotypes of M. chitwoodi cannot be differentiated using the aforementioned techniques. Based on the in silico genome comparison of M. chitwoodi Race 1, Race 2 and Race 1Roza, we developed diagnostic molecular markers that could successfully differentiate between M. chitwoodi races and pathotype. Further, we also developed three race-specific markers that can specifically amplify Race 1, Race 2, or Race 1Roza. Overall, we have potential markers that can successfully differentiate all the two races and one pathotype of M. chitwoodi through simplex PCR, which has potential application in plant disease diagnostics.
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