Isolation and sequence analysis of the wheat B genome subtelomeric DNA

Салина, Е. А.; Sergeeva, E. M.; Адонина, И. Г.; Shcherban, A. B.; Afonnikov, D. A.; Belcram, Harry; Huneau, Cécile; Chalhoub, Boulos

doi:10.1186/1471-2164-10-414

Cited by 23 publications

(33 citation statements)

References 55 publications

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“…The preferred occurrence of 5S rDNA sites in the proximal region and secondarily in the terminal region seems to follow a pattern similar to satellite DNA sequences, which are usually pericentromeric and/or terminal [Paterson et al, 2009;Salina et al, 2009;Barros e Silva et al, 2010;Vogel et al, 2010;Koo et al, 2011]. However, differently from most pericentromeric satellites, frequently widespread in the pericentromeric regions of all chromosomes [Hemleben et al, 2007;Plohl et al, 2008], the proximal 5S rDNA repeats tend to be restricted to a single site.…”

Section: Distribution Of 5s Rdna Sites On Chromosome Armsmentioning

confidence: 99%

Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes

Roa¹,

Guerra²

2015

Cytogenet Genome Res

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5S and 45S rDNA sites are the best mapped chromosome regions in eukaryotic chromosomes. In this work, a database was built gathering information about the position and number of 5S rDNA sites in 784 plant species, aiming to identify patterns of distribution along the chromosomes and its correlation with the position of 45S rDNA sites. Data revealed that in most karyotypes (54.5%, including polyploids) two 5S rDNA sites (a single pair) are present, with 58.7% of all sites occurring in the short arm, mainly in the proximal region. In karyotypes of angiosperms with only 1 pair of sites (single sites) they are mostly found in the proximal region (52.0%), whereas in karyotypes with multiple sites the location varies according to the average chromosome size. Karyotypes with multiple sites and small chromosomes (<3 µm) often display proximal sites, while medium-sized (between 3 and 6 µm) and large chromosomes (>6 µm) more commonly show terminal or interstitial sites. In species with holokinetic chromosomes, the modal value of sites per karyotype was also 2, but they were found mainly in a terminal position. Adjacent 5S and 45S rDNA sites were often found in the short arm, reflecting the preferential distribution of both sites in this arm. The high frequency of genera with at least 1 species with adjacent 5S and 45S sites reveals that this association appeared several times during angiosperm evolution, but it has been maintained only rarely as the dominant array in plant genera.

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Section: Distribution Of 5s Rdna Sites On Chromosome Armsmentioning

confidence: 99%

Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes

Roa¹,

Guerra²

2015

Cytogenet Genome Res

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“…The DNA-transposon Caspar_2050O8, belonging to Caspar_Triticinae, was found previously within BAC_205 0O8, localized to the terminal bin of chromosome 4BL (Salina et al 2009). This element, with a length of 11,666 bp, is the only autonomous element in BAC clone 2050O8; it contains two ORFs characteristic of the Caspar elements, namely the transposase and CTG-2 genes with lengths of 3,363 and 4,105 bp, respectively, and is conWned between a CACTA motif and a target site duplication sequence at the ends of the element.…”

Section: Phylogenetic Analysis Of Triticeae Caspar-like Cacta Mobile mentioning

confidence: 99%

“…Note that the distribution of CACTA DNA-transposons in wheat genomic sequences is not homogeneous. Variation in the content of CACTA DNA-transposons in the characterized Triticum aestivum BAC clones amounts to 0.2-40% of the overall sequence length (Devos et al 2005;Charles et al 2008;Salina et al 2009). …”

Section: Introductionmentioning

confidence: 99%

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Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization

et al. 2010

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Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species.

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“…6 B, C). Other kinds of repetitive DNA, such as pSc119.2 [Badaeva et al, 1996;Molnár et al, 2014;present study] and different types of transposable elements [Raskina et al, 2004a[Raskina et al, , b, 2008Salina et al, 2009Salina et al, , 2011, could be the targets for nonhomologous/illegitimate recombination in virtually any area of the chromatin.…”

Section: Homologous and Nonhomologous Recombination Underlie Genotypementioning

confidence: 99%

Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in <b><i>Aegilops speltoides</i></b> Tausch (Poaceae, Triticeae)

Raskina

2017

Cytogenet Genome Res

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In wild plant populations, chromosome rearrangements lead to the wide intraspecific polymorphisms in the abundance and patterns of highly repetitive DNA. However, despite the large amount of accumulated data, the impact of the complex repetitive DNA fraction on genome reorganization and functioning and the mechanisms balancing and maintaining the structural integrity of the genome are not fully understood. Homologous recombination is thought to play a key role in both genome reshuffling and stabilization, while the contribution of nonhomologous recombination seems to be undervalued. Here, tandem repeat patterns and dynamics during pollen mother cell development were addressed, with a focus on the meiotic recombination that determines chromosome/genome repatterning and stabilization under cross-pollination and artificial hybridization in wild goatgrass, Aegilops speltoides. Native plants from contrasting allopatric populations and artificially created intraspecific hybrids were investigated using a FISH approach. Cytogenetic analysis uncovered a wide spectrum of genotype- and cell-specific chromosomal rearrangements, suggesting intensive repatterning of both parental and hybrid genomes. The data obtained provide evidence that repetitive elements serve as overabundant and ubiquitous resources for maintaining chromosome architecture/genome integrity through homologous and nonhomologous recombination at the intraorganismal level, and genotype-specific repatterning underlies intrapopulation polymorphisms and intraspecific diversification in the wild.

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Isolation and sequence analysis of the wheat B genome subtelomeric DNA

Cited by 23 publications

References 55 publications

Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes

Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes

Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization

Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in <b><i>Aegilops speltoides</i></b> Tausch (Poaceae, Triticeae)

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