Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus

Abstract

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.

Molecular Karyotyping on Populus simonii × P. nigra and the Derived Doubled Haploid

“…BLASTN was performed with tandem repeats, as reported by Rajagopal [ 18 ]. Two candidate tandem repeats with lengths of 129 and 109 bp were identified and named pPC349_XHY and pPD284_XHY ( Table 1 ).…”

“…Highly repetitive sequences are ideal chromosomal markers for chromosome identification. Two repetitive sequences were obtained by homology searching against the P. xiaohei genome sequences using a 145 bp tandem repeat family identified in Populus species [ 18 ]. Two repetitive motifs, 109 and 129 bp, were identified in the P. xiaohei genome.…”

“…Thus, chromosomal variation or polymorphism in or between species can be revealed by exploiting additional repeat markers. Early studies showed that the 145 bp tandem repeat accounts for 1.5% of the genome in P. deltoids [ 18 ]. However, repetitive elements cover over 40% of the assembled genome of P. trichocarpa [ 29 ].…”

Centromere Satellites From Arabidopsis Populations: Maintenance of Conserved and Variable Domains

“…Many studies have compared the satellites from closely related species (Waye and Willard 1989;Grebenstein et al 1996;Alix et al 1998;Mestrovic et al 1998;Rajagopal et al 1999;Landais et al 2000;Nijman and Lenstra 2001). In these analyses, homogenization of satellite repeats within the genome has typically occurred, resulting in less variation within a species than between closely related species.…”

Απομόνωση μικροδορυφόρων στη μεσογειακή μύγα Ceratitis Capitata και η χρησιμοποίηση τους στη φυσική και γενετική χαρτογράφηση του γονιδιώματος του εντόμου

“…gambiae (Biessmann et al, 1999 Jansen et al, 1999), ψάρια (Elder and Turner, 1994), πτηνά (Saifitdinova et al, 2001;Li et al, 2000a), έντοµα (Lorite et al, 2001;He et al, 1998;Perkins et al, 1992) αλλά και φυτά (Wang et al, 2000;Saunders and Houben, 2001;Rajagopal et al, 1999). Η ύπαρξη σε µεγάλη έκταση τέτοιων επαναλαµβανόµενων αλληλουχιών στις περιοχές των πρωτογενών περισφίξεων πιστεύεται ότι παίζει σηµαντικό ρόλο και στη διαµόρφωση της λειτουργία των κεντροµερών.…”