Somatic chromosome karyotype of tomato based on in <i>situ</i> hybridization of the TGRI satellite repeat

Lapitan, Nora L. V.; Ganal, Martin W.; Tanksley, Steven D.

doi:10.1139/g89-543

Cited by 72 publications

(35 citation statements)

References 28 publications

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“…This band is most Biotin-labeled inserts of (A) TGR I and (B) pAtT4 were hybridized to mitotic metaphase chromosomes of tomato. (A) Chromosomes are shown as published in Lapitan et al (1989) according to chromosome number, previously determined using trisomic lines. of Arabidopsis and comprise the most terminal sequences of the tomato chromosomes.…”

Section: Resultsmentioning

confidence: 99%

Macrostructure of the Tomato Telomeres

Ganal¹,

Lapitan²,

Tanksley³

1991

The Plant Cell

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The macrostructure of the tomato telomeres has been investigated by in situ hybridization, genomic sequencing, and pulsed-field gel electrophoresis. In situ hybridizations with a cloned telomeric sequence from Arabidopsis thaliana indicated that the telomeric repeat of tomato cross-hybridizes with that of Arabidopsis and is located at all telomeres. Ba131 digestion kinetics confirmed that the tomato telomeric repeat represents the outermost DNA sequence of each tomato chromosome. Genomic sequencing of enriched tomato telomeric sequences, using primers derived from the Arabidopsis sequence, revealed that the consensus sequence of the tomato telomeric repeat is TT(T/A)AGGG compared with the Arabidopsis consensus sequence of TTTAGGG. Furthermore, as shown by pulsed-field gel electrophoresis, the telomeric repeat of tomato is separated by not more than a few hundred kilobases from a previously described 162-base pair satellite DNA repeat of tomato (TGR I) at 20 of the 24 telomeres. Together, these sequences are found in the heterochromatic terminal knob observed in pachytene chromosomes. Therefore, these two repeats determine the structure of 20 of the 24 tomato chromosome ends over approximately 2% of the total chromosome length.

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Section: Resultsmentioning

confidence: 99%

Macrostructure of the Tomato Telomeres

Ganal¹,

Lapitan²,

Tanksley³

1991

The Plant Cell

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“…matin of the same arm usually cannot be resolved. This problem can be overcome to some extent by using more elongate mitotic prophase chromosomes from aphidicolin-arrested root tip cells [Lapitan et al, 1989]. Another disadvantage of tomato metaphase chromosomes is that most are not identifiable on the basis of relative length and arm ratios.…”

Section: The Structure Of Tomato Chromosomes In Relation To Fish Signalsmentioning

confidence: 99%

Role of Fluorescence in situ Hybridization in Sequencing the Tomato Genome

Stack¹,

Royer²,

Shearer³

et al. 2009

Cytogenet Genome Res

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The tomato (Solanum lycopersicum L.) genome is being sequenced by a consortium of laboratories in 10 countries. Seventy-seven percent of the tomato genome (DNA) is located in repeat-rich, gene-poor, pericentric heterochromatin, while 23% of the genome is located in repeat-poor, gene-rich, distal euchromatin. It is estimated that approximately 90% of tomato’s nuclear genes can be characterized by limiting the sequencing effort to euchromatin while avoiding the problems involved in sequencing the repetitive DNA in heterochromatin. Sequencing is being performed on tomato nuclear DNA cloned into bacterial artificial chromosome (BAC) vectors. Fluorescence in situ hybridization (FISH) is used to help direct the sequencing effort by cytologically demonstrating the location of selected BACs on tomato chromosomes. While mitotic metaphase chromosomes are too short and compact for this purpose, long pachytene chromosomes are ideal. BACs localized in euchromatin can be used confidently as anchors for the assembly of BAC contigs that extend through the euchromatic length of each chromosome arm. Another important role for FISH is identification of BACs near telomeres and near borders with pericentric heterochromatin to indicate that sequencing should not extend much further. This role of FISH is enhanced by our ability to estimate base pair distances between localized BACs and these chromosomal features. Finally, it is noteworthy that when BAC-FISH is combined with chromosomal in situ suppression (CISS) hybridization to block repeats and localize single/low copy sequences, the great majority of BACs localize to single sites. This observation is consistent with tomato being an ancient diploid.

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“…FISH showed that this repeat is present in the heterochromatin of all pericentromeres, but not in the nucleolar organizer regions (NORs) (Zhong et al 1996). Three major genomic repeats, TGRI, TGRII and TGRIII, were described by Schweizer et al (1988), Ganal et al (1988Ganal et al ( , 1991 and Lapitan et al (1989Lapitan et al ( , 1991. It was shown that TGRI is located in the distal regions, and that TGRII and TGRIII are located in the pericentromere heterochromatin regions of the chromosomes.…”

Section: Introductionmentioning

confidence: 99%

“…It was shown that TGRI is located in the distal regions, and that TGRII and TGRIII are located in the pericentromere heterochromatin regions of the chromosomes. Studies of the [TTTAGGG] telomere repeat and the subtelomeric TGRI repeat (Lapitan et al 1989 in pachytene and in extended DNA fibre FISH (Zhong et al 1996(Zhong et al , 1998 revealed accurate distributions and size estimates of these repeats in the chromosome ends and in the long-arms interstitial knobs. Initial low resolution in-situ hybridizations at metaphase complements also identified the TGRII repeat family on nearly all chromosomes except for chromosome 2, whereas TGRIII occurred in the centromere regions of only nine of the chromosomes .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2008

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This paper presents a bird_s-eye view of the major repeats and chromatin types of tomato. Using fluorescence insitu hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA] 4 , a microsatellite that also forms part of the pericentromeres, together with [GA] 8 , [GATA] 4 and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6)

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Somatic chromosome karyotype of tomato based on in situ hybridization of the TGRI satellite repeat

Cited by 72 publications

References 28 publications

Macrostructure of the Tomato Telomeres

Macrostructure of the Tomato Telomeres

Role of Fluorescence in situ Hybridization in Sequencing the Tomato Genome

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

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