Browsing by Author "Kantety, R.V."
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Item 18S and ITS1 genomic sequence variations in Rotylenchulus reniformis isolates from Alabama(Journal of Cotton Science, 2013-01) Nyaku, S.T.; Kantety, R.V.; Tilahun, Y.; Lawrence, K.S.; Soliman, K.M.; Cebert, E.; Sharma, G.C.Upland cotton, Gossypium hirsutum L., is highly susceptible to infection by reniform nematode (Rotylenchulus reniformis), which can cause over 10% reduction of cotton yields in Alabama. Detection of reniform nematode (RN) and analysis for molecular variation within its population is important for understanding its interactions with cotton and other host plant species. Restriction analysis of PCR products of ITS1 regions was achieved using four restriction enzymes, HaeIII, HhaI, MspI, and RsaI. These showed similar banding patterns for both male and female populations. However, MspI digestion of ITS1 amplification products showed variants within the combined sex and location effects primarily attributed to a 500 bp fragment that was absent in other restriction digestions. Intra-nematodal variations in 18S and ITS1 rDNA were studied in detail by sequencing a minimum of ten clones in each individual male and female RN isolates in both directions. Multiple sequence alignment of the 18S rDNA sequences showed two major types of sequences within this gene for both male and female RN clones, which could be distinguished at 27 specific sites. Two distinct ITS1 fragments of lengths (550 bp and 720 bp) were observed; referred to as ITS1S and ITS1L respectively. Neighbor-joining analysis was used in revealing the relationships and grouping characteristics between male and female RN clones, with clones grouping together irrespective of sex and isolate. Sequencing of one-third of the 18S and ITS1 rDNA regions provided clear evidence of intra-and inter-nematode variability, in addition to gene conversion events in the 18S rDNA of individual male and female RN clones. © The Cotton Foundation 2013.Item Canonical discriminant analysis of Rotylenchulus reniformis in Alabama(Nematropica, 2013-01) Nyaku, S.T.; Kantety, R.V.; Lawrence, K.S.; Van Santen, E.; Sharma, G.C.The reniform nematode, Rotylenchulus reniformis, infests over 300 plant species worldwide and over the last two decades it has emerged as a major cotton pest in the southeastern United States. Nine locations in Alabama and one location in Mississippi were selected for study of R. reniformis. Thirteen morphometric measurements were made on 20 male and 20 female nematodes from each population. The sex and location interaction was significant (P < 0.005) for all traits except total body length (P = 0.29) and the derived ratio trait a (body length / maximum body width, P = 0.06). Canonical discriminant analysis effectively separated the 10 sampling locations into three distinct groups; among them, Group 1 and 3 were distinct with an intermediate group (Group 2) differentiating in the middle. Furthermore, both female and male R. reniformis based on the morphometrics measured here adhered to this metrics-based grouping. Belle Mina (Limestone County, AL), Huxford (Escambia County, AL), and Mississippi State University, MSU (Oktibbeha County, MS) locations were separated from the remaining seven locations based on the large positive CAN1 centroid means. Eight out of 13 traits had high phenotypic correlations (r > 0.80) with CAN 1 for both sexes. Anal width and length of the hyaline portion of the tail measurement accounted for a significant amount (r > 80%) of the variation in total and sex-based canonical structure. Occurrence of the three non-overlapping morphometric groups in cotton-growing fields in close proximity (250 mile radius) suggests a greater biological variation in this species than expected. Cotton cultivars with differential resistance and soil types are among the major factors to be tested for further delineating the causes of morphometric variation in R. reniformis.Item Characterization of the reniform nematode genome by shotgun sequencing(Genome, 2014-06) Nyaku, S.T.; Sripathi, V.R.; Kantety, R.V.; Cseke, S.B.; Buyyarapu, R.; Mc Ewan, R.; Gu, Y.Q.; Lawrence, K.; Senwo, Z.; Sripathi, P.; George, P.; Sharma, G.C.The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States, 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 pooled DNA of four adult female RNs and assembled into 67 317 contigs, including 25 904 (38.5%) predicted coding contigs and 41 413 (61.5%) noncoding contigs. Most of the characterized repeats were of low complexity (88.9%), and 0.9% of the contigs matched with 53.2% of GenBank ESTs. The most frequent Gene Ontology (GO) terms for molecular function and biological process were protein binding (32%) and embryonic development (20%). Further analysis showed that 741 (1.1%), 94 (0.1%), and 169 (0.25%) RN genomic contigs matched with 1328 (13.9%), 1480 (5.4%), and 1330 (7.4%) supercontigs of Meloidogyne incognita, Brugia malayi, and Pristionchus pacificus, 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) involved in cell wall degradation were studied in more detail. Additionally, kinases, G protein-coupled receptors, and neuropeptides functioning in physiological, developmental, and regulatory processes were identified in the RN genome. © 2014 Published by NRC Research Press.