Chromosome identification in the Andean common bean accession G19833 (Phaseolus vulgaris L., Fabaceae)

Altrock, Sarah; Fonsêca, Artur; Pedrosa‐Harand, Andrea

doi:10.1590/s1415-47572011005000029

Cited by 10 publications

(12 citation statements)

References 20 publications

(40 reference statements)

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“…These data are in general agreement with the cytogenetic distribution of BAC 63H6, which contains khipu (K.G.B. dos Santos, personal communication) in G19833 (Altrock et al, 2011), except that Chr10S and Chr11S seem to have large amounts of khipu (as estimated based on the intensity of FISH signals) and no khipu signal could be detected in Chr09L. In agreement with previous FISH analysis on BAT93 showing the subtelomeric distribution of khipu (David et al, 2009), khipu units were mainly located in the first or last five megabase-pairs of the pseudomolecules.…”

Section: Resultssupporting

confidence: 86%

“…It is surprising that no centromeric signals were found in previous FISH experiments on mitotic chromosomes, using either a khipu -specific probe in the BAT93 common bean genome (David et al, 2009; Geffroy et al, 2009) or a khipu -bearing subtelomeric BAC clone in G19833 (Altrock et al, 2011). These conflicting results raise the question of whether the centromeric khipu units are real centromeric sequences or misassembled sequences.…”

Section: Resultsmentioning

confidence: 98%

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The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833

et al. 2013

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Subtelomeric regions in eukaryotic organisms are known for harboring species-specific tandemly repeated satellite sequences. However, studies on the molecular organization and evolution of subtelomeric repeats are scarce, especially in plants. Khipu is a satellite DNA of 528-bp repeat unit, specific of the Phaseolus genus, with a subtelomeric distribution in common bean, P. vulgaris. To investigate the genomic organization and the evolution of khipu, we performed genome-wide analysis on the complete genome sequence of the common bean genotype G19833. We identified 2,460 khipu units located at most distal ends of the sequenced regions. Khipu units are arranged in discrete blocks of 2–55 copies and are heterogeneously distributed among the different chromosome ends of G19833 (from 0 to 555 khipus units per chromosome arm). Phylogenetically related khipu units are spread between numerous chromosome ends, suggesting frequent exchanges between non-homologous subtelomeres. However, most subclades contain numerous khipu units from only one or few chromosome ends indicating that local duplication is also driving khipu expansion. Unexpectedly, we also identified 81 khipu units located at centromeres. All the centromeric khipu units belong to a single divergent clade also comprised of a few units from several subtelomeres, suggesting that a few sequence exchanges between centromeres and subtelomeres took place in the common bean genome. The divergence and low copy number of these centromeric units from the subtelomeric units could explain why they were not detected by FISH (Fluorescence in situ Hybridization) although it can not be excluded that these centromeric units may have resulted from errors in the pseudomolecule assembly. Altogether our data highlight extensive sequence exchanges in subtelomeres between non-homologous chromosomes in common bean and confirm that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 98%

The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833

et al. 2013

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“…In Phaseoloid legumes, 18S–5.8S–25S and 5S rDNA distributions were previously observed in Phaseolus species including common bean (Moscone et al, 1999; Pedrosa‐Harand et al, 2006; Altrock et al, 2011), cowpea (Galasso et al, 1995), Glycine species including soybean (Krishnan et al, 2001), winged bean (Chaowen et al, 2004), and pigeonpea (Varshney et al, 2011). Most interestingly, despite the recent whole genome duplication, soybean has only one 18S–5.8S–25S and one 5S rDNA locus, located on separate chromosomes (Krishnan et al, 2001).…”

Section: Chromosomal Distribution Of Ribosomal Dna Genesmentioning

confidence: 70%

Cytogenetics of Legumes in the Phaseoloid Clade

2013

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Cytogenetics played an essential role in studies of chromosome structure, behavior, and evolution in numerous plant species. The advent of molecular cytogenetics combined with recent development of genomic resources has ushered in a new era of chromosome studies that have greatly advanced our knowledge of karyotypic diversity, genome and chromosome organization, and chromosomal evolution in legumes. This review summarizes some of the achievements of cytogenetic studies in legumes in the Phaseoloid clade, which includes several important legume crops such as common bean (Phaseolus, and pigeonpea [Cajanus cajan (L.) Huth]. In the Phaseoloid clade, karyotypes are mostly stable. There are, however, several species with extensive chromosomal changes. Fluorescence in situ hybridization has been useful to reveal chromosomal structure by physically mapping transposons, satellite repeats, ribosomal DNA genes, and bacterial artificial chromosome clones onto chromosomes. Polytene chromosomes, which are much longer than the mitotic chromosomes, have been successfully found and used in cytogenetic studies in some Phaseolus and Vigna species. Molecular cytogenetics will continue to be an important tool in legume genetics and genomics, and we discuss future applications of molecular cytogenetics to better understand chromosome and genome structure and evolution in legumes.

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“…Phaseolus vulgaris (the common bean) is the most important crop species of the genus and has an enormous importance as a food resource for many human populations, especially in Africa and South America. In addition to its economic and nutritional importance, the common bean has been the focus of a number of chromosome evolution studies, making the genus an important model for plants with small genomes and high karyotypic stability [Altrock et al, 2011;Bonifácio et al, 2012;Almeida and Pedrosa-Harand, 2013;Fonsêca and Pedrosa-Harand, 2013]. This species was also used as a model for studying plant-pathogen interactions, especially in the evolution of resistance to anthracnose caused by the fungus Colletotrichum lindemuthianum [Geffroy et al, 1999[Geffroy et al, , 2000[Geffroy et al, , 2008David et al, 2008David et al, , 2009.…”

mentioning

confidence: 99%

Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

Fonsêca

Richard

Geffroy

et al. 2014

Cytogenet Genome Res

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The common bean (Phaseolus vulgaris L.) is the main representative of its genus and one of most important sources of proteins in African and Latin American countries. Although it is a species with a small genome, its pericentromeric and subtelomeric heterochromatin fractions are interspersed with single-copy sequences and active genes, suggesting a less compartmentalized genome organization. The present study characterized its chromatin fractions, associating the distribution of repetitive sequences and resistance genes with histone and DNA epigenetic modifications with and without biotic stress. Immunostaining with H3K4me3 and H4K5ac were generally associated with euchromatic regions, whereas H3K9me2, H3K27me1, and 5mC preferentially labeled the pericentromeric heterochromatin. The 45S rDNA and centromeric DNA sequences were hypomethylated as were most of the terminal heterochromatic blocks. The largest of them, which is associated with resistance genes, was also hypomethylated after the plants were infected with virulent and avirulent strains of the fungus Colletotrichum lindemuthianum, suggesting no correlation with control of resistance gene expression. The results highlighted the differences between subtelomeric and pericentromeric heterochromatin as well as variation within the pericentromeric heterochromatin.

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Chromosome identification in the Andean common bean accession G19833 (Phaseolus vulgaris L., Fabaceae)

Cited by 10 publications

References 20 publications

The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833

The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833

Cytogenetics of Legumes in the Phaseoloid Clade

Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

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