Multiple Divergent ITS1 Copies Were Identified in Single Tomato Genome Using DGGE Analysis

Liu, Bo; Lowes, F. J.

doi:10.1007/s11105-012-0500-0

Cited by 6 publications

(3 citation statements)

References 38 publications

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“…Denaturing gradient gel electrophoresis (DGGE) is a technique that has been widely used in diversity studies of viral genomes ( Short and Suttle, 1999 ; Lyttle et al, 2011 ; Carmona et al, 2012 ), as well as the study of plant genome polymorphisms ( Riedel et al, 1990 ; Liu and Lowes, 2013 ). In DGGE, double stranded and partially denatured DNA differs in its mobility when analysed by polyacrylamide gel electrophoresis and PCR fragments can be differentiated based on single base changes through the addition of a GC clamp ( Sheffield et al, 1989 ; Top, 1992 ; Green et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

et al. 2022

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Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.

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Section: Introductionmentioning

confidence: 99%

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

et al. 2022

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“…The technique detects variation of small DNA fragments (~200–700 bp) that differ by as little as a single base substitution [ 46 , 47 , 48 ]. DGGE has been used extensively for diversity studies such as microbial biodiversity [ 45 , 49 , 50 , 51 ], fungal communities [ 52 ], genomes of viral strains [ 53 , 54 , 55 ], forensic application [ 56 ] and plant genome polymorphisms [ 57 , 58 ].…”

Section: Introductionmentioning

confidence: 99%

PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm

Turaki

Bömer

Silva

et al. 2017

Viruses

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Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.

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“…We used denaturing electrophoresis to assess diversity in non-coding loci of plastid DNA because it seemed to be a simple and cheap tool used previously in plant genetics (Liu & Lowes 2013) for detection of mutations. The primary aim was to determine diversity in selected plastid DNA loci to distinguish Solanum species in the potato genetic resource collection.…”

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confidence: 99%

Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum

Sedláková¹,

Sedlák²,

Zeka³

et al. 2017

CZECH J GENET PLANT

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Sedláková V., Sedlák P., Zeka D., Domkářová J., Doležal P., Vejl P. (2017): Evaluation of variations in plastid DNA noncoding regions in selected species of the genus Solanum. Czech J. Genet. Plant Breed., 53: 127−131.The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with single point mutations in the sequence confirmed by sequencing. The DGGE method was found to be a simple and cheap pre-exploring tool for mutation detection in compared DNA regions. Some identified polymorphisms can be used in the management of genetic resources.

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Multiple Divergent ITS1 Copies Were Identified in Single Tomato Genome Using DGGE Analysis

Cited by 6 publications

References 38 publications

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm

Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum

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