FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato

Abstract

The molecular and cytological organization of the telomeric repeat (TR) and the subtelomeric repeat (TGR1) of tomato were investigated by fluorescence in situ hybridization (FISH) techniques. Hybridization signals on extended DNA fibres, visualized as linear fluorescent arrays representing individual telomeres, unequivocally demonstrated the molecular co-linear arrangement of both repeats. The majority of the telomeres consisted of a TR and a TGR1 region separated by a spacer. Microscopic measurements of the TR and TGR1 signals revealed high variation in length of both repeats, with maximum sizes of 223 and 1330 kb, respectively. A total of 27 different combinations of TR and TGR1 was detected, suggesting that all chromosome ends have their own unique telomere organization. The fluorescent tracks on the extended DNA fibres were subdivided into four classes: (i) TR-spacer-TGR1; (ii) TR-TGR1; (iii) only TR; (iv) only TGR1. FISH to pachytene chromosomes enabled some of the TR/TGR1 groups to be assigned to specific chromosome ends and to interstitial regions. These signals also provided evidence for a reversed order of the TR and TGR1 sites at the native chromosome ends, suggesting a backfolding telomere structure with the TGR1 repeats occupying the most terminal position of the chromosomes. The FISH signals on diakinesis chromosomes revealed that distal euchromatin areas and flanking telomeric heterochromatin remained highly decondensed around the chiasmata in the euchromatic chromosome areas. The rationale for the occurrence and distribution of the TR and TGR1 repeats on the tomato chromosomes are discussed.

FISH mapping and molecular organization of the major repetitive sequences of tomato

“…The species is also recognized for its eminent pachytene morphology (Ramanna & Prakken 1967, Khush & Rick 1968, Zhong et al 1998) and well-differentiated synaptonemal complexes (Sherman & Stack 1995, Peterson et al 1999. Its genome size amounts to 950 Mb (Arumuganathan & Earle 1991) and tomato thus ranks among plant species with middle-sized genomes.…”

Tomato genome sequencing: deciphering the euchromatin region of the chromosome 8

“…We seem to have reached to the euchromatin/heterochromatin border in the distal end of the long arm. Extension from a marker at 87 cM has led us to encounter a clone with long stretch of 162-bp repeat which is the previously identified TGR1, tomato subtelomere-specific repeat (Zhong et al 1998). In some parts, we are currently facing exhaustion of BAC clones to extend.…”

“…The genome size of tomato is estimated to be 950 Mb, which is among the smallest in Solanaceae family. Cytogenetic analyses of the pachytene chromosomes have revealed a largely contiguous euchromatin structure, which comprises approximately 25% of the entire genome (Wang et al 2006;Zhong et al 1998).…”

Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions

“…In the human genome, subtelomeres vary in size from 8 kb up to 300 kb Der-Sarkissian et al 2002), whereas in plant genomes, such as tomato (Broun et al 1992;Zhong et al 1998), rice (Ohmido and Fukui 1997;Ohmido et al 2000Ohmido et al , 2001, and tomato (+) potato hybrids , such regions can measure up to 1,000 kb. The highly variable distribution of large duplicated subtelomeric segments are caused by homology-based, non-allelic (ectopic) recombination events between nonhomologous chromosomes Scherf et al 2001;Der-Sarkissian et al 2002).…”

“…The result has been the integration of 32 of the 96 telomere regions into the human genome draft sequence (Riethman 1997;Riethman et al 2001;Xiang et al 2001). In tomato, species-specific subtelomeric repeats (162-bp unit, TGR1, 500-10,000 copies per locus) have been identified in 20 of the 24 telomeres near the telomere repeat stretch (Ganal et al 1991;Broun et al 1992;Zhong et al 1998). Some subtelomere sequences have also been identified and mapped using a degenerate telomere primer and the Vectorette PCR approach in wheat (Mao et al 1997), barley (Kilian and Kleinhofs 1992;Rö der et al 1993), and rice (Ashikawa et al 1994).…”