Search

Summary: Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X‐ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double‐strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing. [ABSTRACT FROM AUTHOR]

Genome stability is a crucial feature of eukaryotic organisms because its alteration drastically affects the normal development and survival of cells and the organism as a whole. Nevertheless, some organisms can selectively eliminate part of their genomes from certain cell types during specific stages of ontogenesis. This review aims to describe the phenomenon of programmed DNA elimination, which includes chromatin diminution (together with programmed genome rearrangement or DNA rearrangements), B and sex chromosome elimination, paternal genome elimination, parasitically induced genome elimination, and genome elimination in animal and plant hybrids. During programmed DNA elimination, individual chromosomal fragments, whole chromosomes, and even entire parental genomes can be selectively removed. Programmed DNA elimination occurs independently in different organisms, ranging from ciliate protozoa to mammals. Depending on the sequences destined for exclusion, programmed DNA elimination may serve as a radical mechanism of dosage compensation and inactivation of unnecessary or dangerous genetic entities. In hybrids, genome elimination results from competition between parental genomes. Despite the different consequences of DNA elimination, all genetic material destined for elimination must be first recognised, epigenetically marked, separated, and then removed and degraded. [ABSTRACT FROM AUTHOR]

B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes., Our comparative transcriptome analysis and the detection of active RNA polymerase II ( RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye ( Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process., In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies., Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes. [ABSTRACT FROM AUTHOR]

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA ( rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA ( gDNA) and RNA-derived complementary DNA ( cDNA), using part of the ITS2 flanking coding regions (5.8 S and 28 S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them ( Hap4) being specific to a supernumerary ( B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes ( Hap1, Hap2 and Hap5), but significant underexpression for three others ( Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28 S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated. [ABSTRACT FROM AUTHOR]

The red fox (Vulpes vulpes) demonstrates a variety of coat colors including platinum, a common phenotype maintained in farm-bred fox populations. Foxes heterozygous for the platinum allele have a light silver coat and extensive white spotting, whereas homozygosity is embryonic lethal. Two KIT transcripts were identified in skin cDNA from platinum foxes. The long transcript was identical to the KIT transcript of silver foxes, whereas the short transcript, which lacks exon 17, was specific to platinum. The KIT gene has several copies in the fox genome: an autosomal copy on chromosome 2 and additional copies on the B chromosomes. To identify the platinum-specific KIT sequence, the genomes of one platinum and one silver fox were sequenced. A single nucleotide polymorphism (SNP) was identified at the first nucleotide of KIT intron 17 in the platinum fox. In platinum foxes, the A allele of the SNP disrupts the donor splice site and causes exon 17, which is part of a segment that encodes a conserved tyrosine kinase domain, to be skipped. Complete cosegregation of the A allele with the platinum phenotype was confirmed by linkage mapping (LOD 25.59). All genotyped farm-bred platinum foxes from Russia and the US were heterozygous for the SNP (A/G), whereas foxes with different coat colors were homozygous for the G allele. Identification of the platinum mutation suggests that other fox white-spotting phenotypes, which are allelic to platinum, would also be caused by mutations in the KIT gene. [ABSTRACT FROM AUTHOR]

Hybridization has played an important role in Saxifraga evolution causing reticulation and a high number of described hybrids, but little is known about how hybrid speciation had occurred in the genus. We focus on a group of closely related Saxifraga species of the subsection Triplinervium from Pyrenees, the phylogenetic relationships of which remain unsolved. Trying to unmask cryptic (or ancient) hybridization processes, we analyze one nuclear (ITS) and three plastid regions ( rpl32- trnL, trnS- trnG- trnG, and 3′trnV-ndhC), as well as nuclear DNA content. Pollen and seed morphology and viability studies were carried out to evaluate the status of spontaneous hybrids. DNA ploidy levels were also inferred for the two Madeiran taxa (of the same Saxifraga subsection), where recent hybridization processes are not expected. Molecular markers revealed multiple reticulation events, which, as suggested by DNA content and chromosome numbers, have occurred in homoploidy (without genome doubling after hybridization). In addition, autopolyploidy has occurred in some species or populations, especially in the Madeiran archipelago colonization. Chromosome number variation appears to be related to centric fission events, which also could lead to the formation of the B chromosomes inferred in some taxa. Spontaneous hybrids do not produce viable seeds and this could be due to differences in parental chromosome numbers. Hybrid speciation has probably been successful by chromosomal arrangements, which also generated new, more or less intermediate, chromosomal numbers in this group of taxa. [ABSTRACT FROM AUTHOR]

Constitutive heterochromatin represents a substantial portion of the eukaryote genome, and it is mainly composed of tandemly repeated DNA sequences, such as satellite DNAs, which are also enriched by other dispersed repeated elements, including transposons. Studies on the organization, structure, composition and in situ localization of satellite DNAs have led to consistent advances in the understanding of the genome evolution of species, with a particular focus on heterochromatic domains, the diversification of heteromorphic sex chromosomes and the origin and maintenance of B chromosomes. Satellite DNAs can be chromosome specific or species specific, or they can characterize different species from a genus, family or even representatives of a given order. In some cases, the presence of these repeated elements in members of a single clade has enabled inferences of a phylogenetic nature. Genomic DNA restriction, using specific enzymes, is the most frequently used method for isolating satellite DNAs. Recent methods such as C 0 t– 1 DNA and chromosome microdissection, however, have proven to be efficient alternatives for the study of this class of DNA. Neotropical ichthyofauna is extremely rich and diverse enabling multiple approaches with regard to the differentiation and evolution of the genome. Genome components of some species and genera have been isolated, mapped and correlated with possible functions and structures of the chromosomes. The 5S HindIII-DNA satellite DNA, which is specific to Hoplias malabaricus of the Erythrinidae family, has an exclusively centromeric location. The As51 satellite DNA, which is closely correlated with the genome diversification of some species from the genus Astyanax, has also been used to infer relationships between species. In the Prochilodontidae family, two repetitive DNA sequences were mapped on the chromosomes, and the SATH 1 satellite DNA is associated with the origin of heterochromatic B chromosomes in Prochilodus lineatus. Among species of the genus Characidium and the Parodontidae family, amplifications of satellite DNAs have demonstrated that these sequences are related to the differentiation of heteromorphic sex chromosomes. The possible elimination of satellite DNA units could explain the genome compaction that occurs among some species of Neotropical Tetraodontiformes. These topics are discussed in the present review, showing the importance of satellite DNA analysis in the differentiation and karyotype evolution of Actinopterygii. [ABSTRACT FROM AUTHOR]

The concept of the 'nucleotype' embraces aspects of the nuclear DNA that affect the phenotype other than through the coding sequences. In this context, we consider one particular situation, namely DNA variation due to the presence of supernumerary B chromosomes (Bs); these Bs, which are additional to the basic complement of A chromosomes, generate a spectrum of DNA amounts, and thus nucleotypes, within many species. We consider the physiological consequences of carrying extra chromosomes that appear by and large to lack coding sequences, and focus on two species with contrasting case histories: rye (Secale cereale L.) and chives (Allium schoenoprasum L.), which illustrate 'selfish' and 'adaptive' explanations of the persistence of B chromosomes. [ABSTRACT FROM AUTHOR]

This review of supernumerary B chromosome systems in flowering plants deals mainly with work published in the last 15 yr. but also includes older material which has not hitherto been presented systematically. The term B chromosome (B) is defined, and there is an introductory overview dealing with general characteristics and the significance of Bs as a widespread chromosome polymorphism. Detailed sections are then presented covering the occurrence of Bs in different taxa, their structure and molecular organization, their irregular modes of inheritance, their phenotypic effects, population dynamics and origin. Particular attention is paid to the research growth points in molecular analysis of the structure and genome organization of Bs, and to transmission genotypes in the context of their aduptive versus their selfish properties. Where appropriate, reference is also made to likely future lines of research, and also to the usefulness of B chromosomes in genetic analysis and as model systems to study general phenomena of genome organization and evolution, nuclear physiology and architecture, chromosome polymorphism and selfish DNA. [ABSTRACT FROM AUTHOR]

To examine whether or not the 18S.26S ribosomal RNA genes are located on the B chromosomes of rye, we applied conventional and molecular cytological techniques to the B chromosomes of six rye strains, including cultivated, weedy and wild species. The results indicated that the B chromosomes in the rye genome do not generally carry repeats of the 18S.26S rRNA genes detectable at the cytological level. [ABSTRACT FROM AUTHOR]

An accession of Lotus alpinus Schleich. (2n=2x=12) from Turkey in which B chromosomes have been found was studied morphologically and karyologically. Chromosome numbers were observed in 519 cells from nine plants which all exhibited mixoploidy (2n=11, 12, 12+1B, 12+2B and over 20). Keel tip color, stem pubescence, and inflorescence size differed from a collection of this species from Switzerland. While the percentage of total lengths of the chromosome complements and the relative chromosome lengths in the two accessions were very similar, the total complement lengths differed considerably (23.14μm Turkey vs. 29.46 μm Switzerland). This karyological difference is not considered to be the result of the presence of B chromosomes, but probably the result of hybridization between different genotypes. Aborted seed pods were observed which lent credibility to this hypothesis. Plants of this accession may have arisen as a result of hybridization between Lotus corniculatus and/or L. alpinus as both diploid and tetraploid cytotypes are reported in the Turkey collection for these species. The data would lend support for their hybrid origin. [ABSTRACT FROM AUTHOR]