Insertional Polymorphism and Antiquity ofPDR1Retrotransposon Insertions in Pisum Species

Abstract

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 .

Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

“…The reason for this is unclear to us as both species show quite similar low outcrossing rates, broad geographic distributions, and domestication histories. Nevertheless, the values of Q w obtained here, combined with the estimate of population size from Jing et al 2005, are consistent with a credible mutation rate in the range 1.8 3 10…”

“…-10 À10 mutations site À1 yr À1 ) is orders of magnitude lower than the estimated transposition rate of PDR1 of 5 3 10 À7 insertions element À1 yr À1 ( Jing et al 2005).…”

“…In plant genomes retrotransposon insertions are mainly found as nested blocks, either between ''gene islands'' or in centromeric regions largely devoid of genes (Pélissier et al 1995;Sanmiguel et al 1996;Presting et al 1998). The corresponding location(s) of Pisum retrotransposon insertions is not yet clear but a Ty3-gypsy group element hybridizes to multiple dispersed spots on in situ metaphase chromosome spreads (Neumann et al 2001), and most of the identifiable PDR1 insertions in the Pisum genome are either in transposable element DNA or unknown repetitious sequence ( Jing et al 2005). In contrast, the sequence data used here derive from 39 expressed nuclear genes.…”

“…In large plant genomes such as maize and Pisum, retrotransposons are mainly located in intergenic nuclear DNA, and the antiquity of individual insertion events typically lies in the 0.1-5 MYA range (Sanmiguel et al 1998;Jing et al 2005). One aim of the present study was to compare SSAP-based diversity analysis with genebased sequence diversity analysis, to see whether these very different genomic fractions produce similar or different pictures of Pisum diversity.…”

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

“…megasoftware.net) using Kimura's 2 parameter model (http://www.megasoftware.net) using the formula: T ¼ K/2r, where T is time of insertion, K is divergence parameter and r is average substitution rate (taken as Ks value). The molecular clock was calibrated with Ks values of synonymous nucleotide substitution rate calculated by Jing et al, (2005), with 7.0 Â 10 À9 substitutions per site per year.…”