Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome. (8th March 2021)

• Record Type: Journal Article
• Authors: Nyaku, S. T.; Sripathi, V. R.; Lawrence, K.; Sharma, G.
• Other Names: Zukowski Kacper Academic Editor.
• Is Part Of: International journal of genomics. Volume 2021(2021)
• Publication Date: 2021-03-08
• Subjects: Genomes -- Periodicals; Genomics -- Periodicals; Cytogenetics -- Periodicals; Genomics; Genome; Molecular Biology; Cytogenetics; Genomes; Genomics; Periodicals; 572.86
• DOI: 10.1155/2021/5532885
• Languages: English
• ISSNs: 2314-436X

Abstract

Abstract : One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis . Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28, 784 and 24, 508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.