AT-rich sequences containing Arabidopsis-type telomere sequence and their chromosomal distribution in Pinus densiflora

Abstract

Japanese red pine Pinus densiflora has 2 n=24 chromosomes and after FISH-detection of Arabidopsis-type (A-type) telomere sequences, many telomere signals were observed on these chromosomes at interstitial and proximal regions in addition to the chromosome ends. These interstitial and proximal signal sites were observed as DAPI-positive bands, suggesting that the interstitial and proximal telomere signal sites are composed of AT-rich highly repetitive sequences. Four DNA clones (PAL810, PAL1114, PAL1539, PAL1742) localized at the interstitial telomere signals were selected from AluI-digested genomic DNA library using colony blot hybridization probed with A-type telomere sequences and characterized using FISH and Southern blot hybridization. The AT-contents of these selected four clones were 60.8-76.3%, and repeat units of the telomere sequence and degenerated telomere sequences were found in their nucleotide sequences. Except for two sites of PAL1114, FISH signals of the four clones co-localized with interstitial and proximal A-type telomere sequence signals. FISH signals a showed similar distribution pattern, but the patterns of signal intensity were different among the four clones. PAL810, PAL1539 and PAL 1742 showed similar FISH signal patterns, and the differences were only with respect to the signal intensity of some signal sites. PAL1114 had unique signals that appeared on chromosomes 7 and 10. Based on results of the Southern blot hybridization these four sequences are not arranged tandemly. Our results suggest that the interstitial A-type telomere sequence signal sites were composed of a mixture of several AT-rich repetitive sequences and that these repetitive sequences contained A-type telomere sequences or degenerated A-type telomere sequence repeats.

Heterochromatin diversity and its co-localization with 5S and 45S rDNA sites in chromosomes of four Maxillaria species (Orchidaceae)

“…the presence of one or more families of tandemly repetitive DNA sequences. Such repeat families can be recognized by different fluorochromes or by fluorescent in situ hybridization (FISH) (Cuadrado and Schwarzacher, 1998;Shibata et al, 2005).…”

A Comparative Analysis of Multi-Probe Fluorescence <i>In Situ</i> Hybridisation (FISH) Karyotypes in 26 <i>Pinus</i> Species (Pinaceae)

“…Data on banding patterns can be used for comparative karyotyping in some species, and they detect inter-and intraspecific variation patterns (Hizume et al 1983(Hizume et al , 1989(Hizume et al , 1990; however, fluorescent banding does not provide sufficient information for the discrimination of all homologous chromosome pairs. Not all homologous pairs in Pinus species were identified by probe signals in studies of karyotypes by FISH that used 35S rDNA and 5S rDNA probes (Doudrick et al 1995, Liu et al 2003, Cai et al 2006, Bogunić et al 2011, telomere sequences (Fuchs et al 1995, Shibata et al 2005, Islam-Faridi et al 2007, or simple sequence repeats (SSR) (Pavia et al 2014). Combined fluorescent banding and FISH investigations have identified interstitial and proximal CMA bands that are consistent with 35S rDNA and/or the short repetitive sequence proximal CMA band-specific repeat (PCSR) loci, and interstitial DAPI bands that are consistent with signals of repetitive sequences containing the Arabidopsis-type telomere sequence (Hizume et al 2001, Shibata et al 2005.…”

“…Not all homologous pairs in Pinus species were identified by probe signals in studies of karyotypes by FISH that used 35S rDNA and 5S rDNA probes (Doudrick et al 1995, Liu et al 2003, Cai et al 2006, Bogunić et al 2011, telomere sequences (Fuchs et al 1995, Shibata et al 2005, Islam-Faridi et al 2007, or simple sequence repeats (SSR) (Pavia et al 2014). Combined fluorescent banding and FISH investigations have identified interstitial and proximal CMA bands that are consistent with 35S rDNA and/or the short repetitive sequence proximal CMA band-specific repeat (PCSR) loci, and interstitial DAPI bands that are consistent with signals of repetitive sequences containing the Arabidopsis-type telomere sequence (Hizume et al 2001, Shibata et al 2005. A FISH probe combining 35S rDNA, 5S rDNA, the Arabidopsis-type telomere sequence, and the PCSR distinguished all homologous pairs in four Pinus species, thereby allowing karyotype comparisons among these species (Hizume et al 2002).…”

Genomics applied to the study of adaptation in pine species

“…Karyotype studies of different pine species have been performed using FISH and fluorescence banding pattern analysis (Doudrick et al, 1995;Jacobs et al, 2000;Hizume et al, 2002;Friesen et al, 2001;Shibata et al, 2005). Different probes, such as telomere and centromeric repeats as well as rDNA and retrotransposon sequences were used to analyse their distribution.…”