A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis

Lee, D.; Ellis, Noel; Turner, L.; Hellens, Roger P.; Cleary, W. G.

doi:10.1007/bf00016121

Cited by 69 publications

(67 citation statements)

References 44 publications

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“…This is a matter of convenience, and nonselective primers could be substituted where the enzyme used for digestion has a larger recognition sequence, or if the copy number were lower. In general, LTR ends are convenient for the design of SSAP primers [ 26 ]. However, for the PDR1 retrotransposon in Pisum , the LTR is exceptionally short at 156 bp, so a GC-rich primer could be designed corresponding to the polypurine tract (PPT) which is found internal to the 3′ LTR in retrotransposons.…”

Section: Introductionmentioning

confidence: 99%

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Kalendar

Schulman

2013

Methods in Molecular Biology

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Retrotransposons are a major component of virtually all eukaryotic genomes, which makes them useful as molecular markers. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplifi cation between the retrotransposon termini and some component of fl anking genomic DNA. The main methods of IRAP, REMAP, RBIP, and SSAP all detect the polymorphic sites at which the retrotransposon DNA is integrated into the genome. Marker systems exploiting these methods can be easily developed and are inexpensively deployed in the absence of extensive genome sequence data. Here, we describe protocols for the IRAP, REMAP, and iPBS techniques, including methods for PCR amplifi cation with a single primer or with two primers, and agarose gel electrophoresis of the product using optimal electrophoresis buffers; we also describe iPBS techniques for the rapid isolation of retrotransposon termini and full-length elements.

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Section: Introductionmentioning

confidence: 99%

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Kalendar

Schulman

2013

Methods in Molecular Biology

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“…At present, rather little genomic sequence is available for Pisum but the repetitious DNAs of the genus are better understood. A variety of retrotransposons, transposons, and other repetitious DNAs have been characterized for Pisum (Lee et al 1990;Chavanne et al 1998;Nouzova et al 2000;Neumann et al 2001Neumann et al , 2003Macas et al 2003). Pea is a predominantly inbreeding Old World legume crop first cultivated 10,000 years ago (Blixt 1972;Zohary 1996;Mithen 2003).…”

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confidence: 99%

“…PDR1 was the first Ty1-copia group retrotransposon to be isolated from Pisum (Lee et al 1990) and remains the best understood. It is one of the smallest and simplest transposition-competent LTR retrotransposons known, with 156-bp LTRs and the typical gag-pr-int-rt-rnaseH gene order of the Ty1-copia group.…”

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confidence: 99%

“…It is one of the smallest and simplest transposition-competent LTR retrotransposons known, with 156-bp LTRs and the typical gag-pr-int-rt-rnaseH gene order of the Ty1-copia group. PDR1 is present across the entire Pisum genus in 200 dispersed copies per haploid genome (Lee et al 1990;Ellis et al 1998) and .95% of insertions are polymorphic within the genus Vershinin et al 2003). Linkage mapping has shown it to be broadly distributed within the Pisum genome .…”

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Insertional Polymorphism and Antiquity ofPDR1Retrotransposon Insertions in Pisum Species

et al. 2005

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Sequences flanking 73 insertions of the retrotransposon PDR1 have been characterized, together with an additional 270 flanking regions from one side alone, from a diverse collection of Pisum germ plasm. Most of the identified flanking sequences are repetitious DNAs but more than expected (7%) lie within nuclear gene protein-coding regions. The approximate age of 52 of the PDR1 insertions has been determined by measuring sequence divergence among LTR pairs. These data show that PDR1 transpositions occurred within the last 5 MY, with a peak at 1-2.5 MYA. The insertional polymorphism of 68 insertions has been assessed across 47 selected Pisum accessions, representing the diversity of the genus. None of the insertions are fixed, showing that PDR1 insertions can persist in a polymorphic state for millions of years in Pisum. The insertional polymorphism data have been compared with the age estimations to ask what rules control the proliferation of PDR1 insertions in Pisum. Relatively recent insertions (, 1.5MYA) tend to be found in small subsets of the Pisum accessions set, ''middle-aged'' insertions (between 1.5 and 2.5 MYA) vary greatly in their occurrence, and older insertions (. 2.5 MYA) are mostly found in small subsets of Pisum. Finally, the average age estimate for PDR1 insertions, together with an existing data set for PDR1 retrotransposon SSAP markers, has been used to derive an estimate of the effective population size for Pisum of 7.5 3 10 5 .

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“…Relativel)^ few of these sequences have been characterized at the DNA sequence level, or in terms of their genomic location (Lee et al, 1990;Ellis et al, 1992;Ellis, 1993). Those repeats which have been characterized are of recognizable DNA sequence classes such as satellite DNAs (Ellis et al, 1989), simple sequence repeats (Lu et al, 1996), 5SrRNA genes (Ellis et al, 1988), rDNA (Ellis et al, 1984;Polans, Weeden & Thompson, 1986), Tycopia like elements (Lee et al, 1990;Flavell, Smith & Kumar, 1992), Ty3-gypsy like elements (Sarup & Stafstrom, 1995), and sequences related to class II transposable elements (Bhattacharyya et al, 1990;Sirsat, 1988;Bown, 1992). From these analyses, the pea genome seems typical of a eukaryotic genome with a size similar to the human genome.…”

Section: Introductionmentioning

confidence: 99%

Repeated sequence markers in pea (Pisum sativum)

Turner

Ellis

1997

New Phytologist

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SUMMARYMultiple-marker techniques based on PCR are highly informative in genetic analysis. The bulk of many genomes is comprised of repeated sequences, and thus anonymous markers derived from genomic DNA are likely to correspond to repeated DNA sequences. Here we show that repeated-sequence-derived markers can provide information similar in quality to that of other PCR-based markers. Presumably this reflects the abundance of this repeat type in anonymous PCR markers such as RAPDs or AFLPs.

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A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis

Cited by 69 publications

References 44 publications

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Insertional Polymorphism and Antiquity ofPDR1Retrotransposon Insertions in Pisum Species

Repeated sequence markers in pea (Pisum sativum)

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