Plant-parasitic nematodes are responsible for annual crop losses in excess of USD123 billion worldwide. Most important are the root-knot nematodes (RKN: Meloidogyne spp.), which establish an intimate association with their host. As a genus, Meloidogyne has a host-range that spans the tracheophyta, although individual isolates are more restricted. In cool climates, M. hapla and M. chitwoodi predominate and are a significant problem on potato in Europe and the US. Because of its genetic tractability, we selected M. hapla for sequencing, and an annotated public release (HapPep1) was made in 2008 (Opperman et al., 2008). Since then we have undertaken on-going curation, and the current release (HapPep5) includes ~2xE9 RNA-Seq reads (Guo et al., 2014). We have also sequenced two additional strains of M. hapla (VW8 and LM) but they have not yet been released. Because M. hapla and M. chitwoodi are sympatric, they presumably have similar gene compliments. To test this, we sequenced the M. chitwoodi genome.Genomic DNA was isolated from nematodes collected in a potato field in Washington State, and confirmed by Axel Elling to be M. chitwoodi. Using an Illumina MiSeq II we obtained 20,079,197 short (~300 bp) paired-end reads. The assembly parameters were empirically optimized, and 4,735 contigs assembled; N50 is 82 kbp. The longest is ~758 kbp with coverage of 33 reads per bp. Average coverage genome-wide is 289 reads. At the protein level, CEGMA identified 245 (98.79%) of the core proteins, pointing to near 100% genome coverage. When CEGMA proteins as a query were blasted against the assembled contigs as a database, it was observed that one protein had hits with more than two contigs. Using CEGMA (and other) proteins, as well as M. chitwoodi ESTs, we trained AUGUSTUS for gene prediction. GO categorization was performed using InterProScan. Analysis of these data is in progress, with an emphasis on genes encoding replicas of plant peptide hormones (xenomones). Because of a potential role in speciation of the closely-related parasites, we have, in collaboration with David Lunt (University of Hull), examined the numbers and distribution of transposable elements: not surprising, M. chitwoodi is much more similar to M. hapla than it is to M. incognita.Operman et al., 2008. Proc Nat Acad Sci 105: 14802 -14807.Guo et al. 2014. Worm 3:
e29158.