Chromosome painting in <i>Arabidopsis thaliana</i>

Lysak, Martin A.; Fransz, Paul; Ali, Hoda Badry Mohammed; Schubert, Ingo

doi:10.1046/j.1365-313x.2001.01194.x

Cited by 156 publications

(108 citation statements)

References 47 publications

Supporting

Mentioning

106

Contrasting

Order By: Relevance

“…The triplication of the At4-b BAC contig together with the comparative genetic mapping that revealed six copies of A. thaliana sequences in Brassica species (Lagercrantz and Lydiate 1996;Cavell et al 1998;Lagercrantz 1998;Parkin et al 2002Parkin et al , 2003 and less comprehensive previous FISH data (Jackson et al 2000; Ziolkowski and Sadowski 2002) suggest a hexaploid ancestor for the Brassiceae tribe. The presumed hexaploidization should not be confused with the genome duplications preceding the origin of Brassicaceae and evident in the A. thaliana genome (Bovers et al 2003) that are no longer detectable by cytogenetic means (Lysak et al 2001). Homeologous recombination in an allotetraploid, followed by imbalanced segregation of the products (Osborn 2004), should yield two instead of three labeled regions on pachytene chromosome complements.…”

Section: Discussionmentioning

confidence: 99%

“…Entire inflorescences were fixed in ethanol/ chloroform/acetic acid (6:3:1) fixative. Spreads of nuclei in meiotic stages (pachytene) were done as described (Lysak et al 2001(Lysak et al , 2003 and treated with pepsin (100 µg/mL 0.01 HCl) prior to FISH.…”

Section: Plant Materialsmentioning

confidence: 99%

“…Subcontigs A-C cover the same chromosome regions as contigs V and VI in C. rubella, I-III in C. bursa-pastoris, and IV-VIII in Arabis alpina used by Lysak et al (2003). For selection of individual BAC clones in each subcontig, see Lysak et al (2001). DNA isolated by a standard alkaline extraction from individual BAC clones was labeled by biotin-dUTP, digoxigenindUTP, and Cy3-dUTP, respectively, via nick translation.…”

Section: Dna Probes and Multicolor Fishmentioning

confidence: 99%

See 2 more Smart Citations

Chromosome triplication found across the tribe Brassiceae

Lysak¹,

Koch²,

Pečinka³

et al. 2005

Genome Res.

Self Cite

608

519

View full text Add to dashboard Cite

We have used an ∼8.7-Mb BAC contig of Arabidopsis thaliana Chromosome 4 to trace homeologous chromosome regions in 21 species of the family Brassicaceae. Homeologs of this segment could be identified in all tested species. Painting of pachytene chromosomes of Calepina, Conringia, and Sisymbrium species (2n = 14, 16), traditionally placed in tribe Brassiceae, showed one homeologous copy of the Arabidopsis contig, while the remaining taxa of the tribe (2n = 14-30) revealed three, and three Brassica species (2n = 34, 36, and 38) and Erucastrum gallicum (2n = 30) had six copies corresponding to the 8.7-Mb segment. The multiple homeologous copies corresponded structurally to the Arabidopsis segment or were rearranged by inversions and translocations within the diploidized genomes. These chromosome rearrangements accompanied by chromosome fusions/fissions led to the present-day chromosome number variation within the Brassiceae. Phylogenetic relationships based on the chloroplast 5Ј-trnL (UAA)-trnF(GAA) region and estimated divergence times based on sequence data of the chalcone synthase gene are congruent with comparative painting data and place Calepina, Conringia, and Sisymbrium outside the clade of Brassiceae species with triplicated genomes. Most likely, species containing three or six copy pairs descended from a common hexaploid ancestor with basic genomes similar to that of Arabidopsis. The presumed hexaploidization event occurred after the Arabidopsis-Brassiceae split, between 7.9 and 14.6 Mya.[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper:The Brassiceae is one of the most morphologically distinct tribes within the Brassicaceae family (Cruciferae). The Brassiceae tribe is a monophyletic group (e.g., Warwick and Black 1997a,b; Anderson and Warwick 1999) comprising ∼240 species in 49-54 genera (Gómez-Campo 1999;Warwick et al. 2000), and includes economically important Brassica crops. Although the basic genome structure of six Brassica crop species was unraveled early (e.g., U 1935), there is a long-lasting debate on the origin and evolution of karyotypes in the genus Brassica and the tribe Brassiceae. The variation in basic chromosome numbers (x = 6-18) (Warwick et al. 2000) makes it difficult to decide whether species with higher basic chromosome numbers are genuine diploids or polyploids. In many Brassiceae genera, species with the lowest chromosome number are considered as diploid. Several hypotheses on ancestral basic numbers (x = 3-7) and karyotype evolution in the Brassiceae have been put forward (for review, see Prakash and Hinata 1980;Truco et al. 1996;Anderson and Warwick 1999;Prakash et al. 1999). However, without knowing phylogenetic relationships and the history of polyploidy of the Brassiceae, unambiguous conclusions cannot be drawn.Already early studies suggested that diploid Brassica species represent "balanced secondary polyploids" exhibiting internal chromosome homeology and genome duplications (e.g., Catcheside 1934;Röbbelen 196...

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

Section: Dna Probes and Multicolor Fishmentioning

confidence: 99%

See 1 more Smart Citation

Chromosome triplication found across the tribe Brassiceae

Lysak¹,

Koch²,

Pečinka³

et al. 2005

Genome Res.

Self Cite

608

519

View full text Add to dashboard Cite

show abstract

“…BAC clones were used as FISH probes for genic regions in species with small genomes and a low content of repetitive elements, such as Arabidopsis (Lysak et al 2001), Brachypodium (Febrer et al 2010;Ma et al 2010), rice , and sorghum (Woo et al 1994;Kim et al 2002). Bread wheat has one of the largest plant genomes (17 Gb), containing about 90% repetitive sequences, 70% of which are transposable elements and a large fraction of microsatellites and tandem repeats (Li et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat

2012

View full text Add to dashboard Cite

“…FISH experiments were carried out as described (16,28). FISH preparations were examined on a Zeiss Axioplan by using 4Ј,6-diamidino-2-phenylindole, FITC, and Texas red fluorescence filter blocks.…”

mentioning

confidence: 99%

Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate

Fransz

Jong

Lysak

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

421

442

View full text Add to dashboard Cite

Heterochromatin in the model plant Arabidopsis thaliana is confined to small pericentromeric regions of all five chromosomes and to the nucleolus organizing regions. This clear differentiation makes it possible to study spatial arrangement and functional properties of individual chromatin domains in interphase nuclei. Here, we present the organization of Arabidopsis chromosomes in young parenchyma cells. Heterochromatin segments are organized as condensed chromocenters (CCs), which contain heavily methylated, mostly repetitive DNA sequences. In contrast, euchromatin contains less methylated DNA and emanates from CCs as loops spanning 0.2-2 Mbp. These loops are rich in acetylated histones, whereas CCs contain less acetylated histones. We identified individual CCs and loops by fluorescence in situ hybridization by using rDNA clones and 131 bacterial artificial chromosome DNA clones from chromosome 4. CC and loops together form a chromosome territory. Homologous CCs and territories were associated frequently. Moreover, a considerable number of nuclei displayed perfect alignment of homologous subregions, suggesting physical transinteractions between the homologs. The arrangement of interphase chromosomes in Arabidopsis provides a well defined system to investigate chromatin organization and its role in epigenetic processes.

show abstract

Chromosome painting in Arabidopsis thaliana

Cited by 156 publications

References 47 publications

Chromosome triplication found across the tribe Brassiceae

Chromosome triplication found across the tribe Brassiceae

Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat

Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate

Contact Info

Product

Resources

About