Location: Crop Improvement and Genetics ResearchTitle: Characterization of reniform nematode genome through shotgun sequencing Author
Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2014
Publication Date: 6/13/2014
Citation: Nyaku, S.T., Sripathi, V.R., Kateny, R.V., Cseke, S.B., Buyyarapu, R., Mcewan, R., Gu, Y.Q., Lawrence, K., Sripathi, P., George, P., Sharma, G.C. 2014. Characterization of reniform nematode genome through shotgun sequencing. Genome. DOI: 10.1139/gen-20140019. Interpretive Summary: The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States(U.S.), is among the major plant parasitic nematodes for which limited genomic information exists. This nematode causes an estimated annual loss of $100M in the U.S. alone. Methods for partially managing RN include crop rotation and the use of nematicides, but only part of profit loss to this nematode is recovered. The objective of this study is to characterize the RN genome by sequencing four adult reniform nematodes through 454 shotgun sequencing and then utilize RN genome sequence data to perform functional analysis to identify candidate parasitism genes. Seven putative detoxification genes and three carbohydrate active enzymes active in cell wall degradation were identified and characterized in detail. Additionally, kinases, G protein coupled receptors (GPCRs), and neuropeptides functioning in the physiological, developmental, and regulatory processes were also identified in the RN genome.
Technical Abstract: The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States(U.S.), is among the major plant parasitic nematodes for which limited genomic information exists. In this study, over 380 Mb of sequence data were generated from four pooled adult female RN and assembled into 67,317 contigs. Total predicted coding contigs were 25,904 (38.5%) and non-coding contigs 41,413 (61.5%). The highest repeats characterized were of low complexity (88.9%), and 0.9% of these contigs matched with 3.2% of GenBank ESTs. The highest gene ontology (GO) distributions for molecular function and biological process were for protein binding (32%) and embryonic development (20%). Further analysis showed 741 (1.1%), 94 (0.1%), and 169 (0.25%) of RN genomic contigs matched with 1,328 (13.9%), 1,480 (5.4%), and 1,330 (7.4%) for Meloidogyne incognita, Brugia malayi, and Pristionchus pacificus super contigs, respectively. Chromosome 5 of Caenorhabditis elegans had the highest number of hits to the RN contigs. Seven putative detoxification genes and three carbohydrate active enzymes (CaZymes) active in cell wall degradation were studied in more detail. Additionally, kinases, Gprotein coupled receptors (GPCRs), and neuropeptides functioning in the physiological, developmental and regulatory processes were identified in the RN genome.