Analysis of high-identity segmental duplications in the grapevine genome

<p>Abstract</p> <p>Background</p> <p>Segmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (<it>Vitis vinifera</it>) genome (PN40024).</p> <p>Results</p> <p>We demonstrate that recent SDs (> 94% identity and >= 10 kb in size) are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence). We detected mitochondrial and plastid DNA and genes (10% of gene annotation) in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress.</p> <p>Conclusions</p> <p>These data show the great influence of SDs and organelle DNA transfers in modeling the <it>Vitis vinifera </it>nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.</p

Molecular genetics and cytogenetics of breast carcinomas: comparison of the two methods

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldMolecular genetics and cytogenetics are two different approaches to studying genetic changes in breast carcinoma. We have used karyotype analysis, fluorescence in situ hybridization, and molecular analysis of allelic imbalance on chromosomes 7q and 16q and on both arms of chromosome 17, to study 85 breast carcinomas. Twenty-five of these samples gave results that could be used to compare the two methods. Sixty-nine chromosome arms were compared, of which 48 (70%) gave concordant molecular and cytogenetical results. Samples were processed for karyotyping both by harvesting directly from the fresh tissue and after selective culture for a few days. Karyotypes among the direct harvest samples matched significantly better with the molecular genetics results than karyotypes among the cultured cell preparations

p53 abnormality and chromosomal instability in the same breast tumor cells

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldTo clarify the important role of the tumor-suppressor gene p53 in maintaining genetic integrity, we estimated chromosome instability and staining of overexpressed p53 protein in the same cells of five primary breast carcinomas. The method included both fluorescence immunohistochemistry and fluorescence in situ hybridization (FISH) on sections from formalin-fixed, paraffin-embedded breast cancer tissue. By using a centromeric FISH probe for chromosome 17 on interphase cells in these sections, we showed that cells with abnormal p53 protein expression had a statistically significant higher number of chromosome 17 than did cells with no p53 protein staining in the same samples as well as cells in four other tumor samples with no p53 protein staining. The samples identified positive for p53 abnormality by immunostaining were shown to have p53 mutation by constant denaturing gel electrophoresis analysis and DNA sequencing. These mutated samples were characterized by high DNA index, high S-phase, abnormal karyotype, and aneuploidy. The results strongly implicate p53 mutation as a cause for chromosomal instability and a crucial step in mammary carcinogenesis

BRCA2 and p53 mutations in primary breast cancer in relation to genetic instability

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldThe products of the BRCA breast cancer susceptibility genes have been implicated in cell cycle control and DNA repair. It has been suggested that mutations in the p53 gene are a necessary step in tumorigenesis in BRCA tumors. We tested samples from 402 breast cancer patients for germ-line BRCA2 and p53 mutations in tumors. p53 mutations are more frequent in BRCA2 mutation carriers than they are in controls. Tumors with mutations in either gene had multiple chromosomal abnormalities, as shown by cytogenetic analysis

Icelandic Birch polyploids - the case of a perfect fit in genome size

Two birch species coexist in Iceland, dwarf birch Betula nana and tree birch B. pubescens. Both species are variablemorphologically, which has been shown to be due to introgressive hybridization via interspecific hybrids. The aim of this study was to examine if the introgression could be related to genome size. We characterized 42 plants from Bifröst woodland morphologically and cytogenetically. The population consisted of diploid B. nana (38%), tetraploid B. pubescens (55%), and triploid hybrids (7%). Genome size wasmeasured from 12 plants, using Feulgen DNA image densitometry (FDM) on spring leaf buds and flow cytometry (FCM) with dormant winter twigs. The use of winter twigs for FCM is novel. The average 1C-values for diploid, triploid, and tetraploid plants were 448, 666, and 882 Mbp, respectively. Monoploid genome sizes were found to be statistically constant among ploidy levels. This stability is in contrast to the different taxonomic positions of the di- and tetraploids and also contrasts with the frequent occurrence of genome downsizing in polyploids