Two Intra-Individual ITS1 rDNA Sequence Variants Identified in the Female and Male Rotylenchulus reniformis Populations of Alabama

Seloame T Nyaku; Sowndarya Karapareddy; Ernst Cebert; Kathy Lawrence; John S Y Eleblu; Govind C Sharma; Venkateswara R Sripathi

doi:10.3390/plants13010005

Two Intra-Individual ITS1 rDNA Sequence Variants Identified in the Female and Male Rotylenchulus reniformis Populations of Alabama

Plants (Basel). 2023 Dec 19;13(1):5. doi: 10.3390/plants13010005.

Authors

Seloame T Nyaku¹, Sowndarya Karapareddy², Ernst Cebert², Kathy Lawrence³, John S Y Eleblu⁴, Govind C Sharma², Venkateswara R Sripathi²

Affiliations

¹ Department of Crop Science, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 44, Ghana.
² Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL 35811, USA.
³ Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA.
⁴ West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 30, Ghana.

Abstract

Around 300 different plant species are infected by the plant-parasitic reniform nematode (Rotylenchulus reniformis), including cotton. This is a devasting nematode with a preference for cotton; it is commonly found in Alabama farms and causes severe reduction in yields. Its first internal transcribed spacer (ITS1) region can be sequenced, and potential mutations can be found in order to study the population dynamics of the reniform nematode. The goal of our study was to sequence the ITS1 rDNA region in male and female RNs that were collected from BelleMina, Hamilton, and Lamons locations in Alabama. After separating the single male and female RNs from the samples collected from the three selected listed sites above, the ITS1 region was amplified selectively using specific primers, and the resulting products were cloned and sequenced. Two distinct bands were observed after DNA amplification of male and female nematodes at 550 bp and 730 bp, respectively. The analysis of sequenced fragments among the three populations showed variation in average nucleotide frequencies of female and male RNs. Singletons within the female and male Hamilton populations ranged from 7.8% to 10%, and the variable sites ranged from 13.4% to 26%. However, female and male BelleMina populations had singletons ranging from 7.1% to 19.7% and variable regions in the range of 13.9% to 49.3%. The female and male Lamons populations had singletons ranging from 2.5% to 8.7% and variable regions in the range of 2.9% to 14.2%. Phylogenetic (neighbor-joining) analysis for the two ITS1 fragments (ITS-550 and ITS-730) showed relatively high intra-nematode variability. Different clone sequences from an individual nematode often had greater similarity with other nematodes than with their own sequences. RNA fold analysis of the ITS1 sequences revealed varied stem and loop structures, suggesting both conserved and variable regions in the variants identified from female and male RNs, thus underscoring the presence of significant intra- and inter-nematodal variation among RN populations in Alabama.

Keywords: Alabama; ITS1; female; male; nematode; population; reniform; sequence; variants.

Abstract

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