Observations on the effects of a chromosome duplication in Aspergillus nidulans

Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola

Meiosis in the haploid plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs and do not pair during meiosis. Because these chromosomes are not present universally in the genome of the organism they can be considered to be dispensable. To analyze the meiotic transmission of unequal chromosome numbers, two segregating populations were generated by crossing genetically unrelated parent isolates originating from Algeria and The Netherlands that had pathogenicity towards durum or bread wheat, respectively. Detailed genetic analyses of these progenies using high-density mapping (1793 DArT, 258 AFLP and 25 SSR markers) and graphical genotyping revealed that M. graminicola has up to eight dispensable chromosomes, the highest number reported in filamentous fungi. These chromosomes vary from 0.39 to 0.77 Mb in size, and represent up to 38% of the chromosomal complement. Chromosome numbers among progeny isolates varied widely, with some progeny missing up to three chromosomes, while other strains were disomic for one or more chromosomes. Between 15–20% of the progeny isolates lacked one or more chromosomes that were present in both parents. The two high-density maps showed no recombination of dispensable chromosomes and hence, their meiotic processing may require distributive disjunction, a phenomenon that is rarely observed in fungi. The maps also enabled the identification of individual twin isolates from a single ascus that shared the same missing or doubled chromosomes indicating that the chromosomal polymorphisms were mitotically stable and originated from nondisjunction during the second division and, less frequently, during the first division of fungal meiosis. High genome plasticity could be among the strategies enabling this versatile pathogen to quickly overcome adverse biotic and abiotic conditions in wheat fields.

Genetic analysis of an unequal chromosomal translocation in Aspergillus nidulans

Translocation T(III–VIII) in Aspergillus nidulans has been analysed by the detection of meiotic linkage between markers previously located separately on linkage groups III and VIII. The breakage points have been mapped by the detection of linkage between the crinkled type and genetic markers in the region of the break. A segment from linkage group III, approximately 43 units long and including the markers moC96, sC12, sA1 and cnxH3, has been translocated into linkage group VIII. The breakage point is between su6proA and moC96 and the attachment point is close to cha in linkage group VIII. It seems probable that the segment has been inserted into linkage group VIII.

Stability of large segmental duplications in the yeast genome

The high level of gene redundancy that characterizes eukaryotic genomes results in part from segmental duplications. Spontaneous duplications of large chromosomal segments have been experimentally demonstrated in yeast. However, the dynamics of inheritance of such structures and their eventual fixation in populations remain largely unsolved. We analyzed the stability of a vast panel of large segmental duplications in Saccharomyces cerevisiae (from 41 kb for the smallest to 268 kb for the largest). We monitored the stability of three different types of interchromosomal duplications as well as that of three intrachromosomal direct tandem duplications. In the absence of any selective advantage associated with the presence of the duplication, we show that a duplicated segment internally translocated within a natural chromosome is stably inherited both mitotically and meiotically. By contrast, large duplications carried by a supernumerary chromosome are highly unstable. Duplications translocated into subtelomeric regions are lost at variable rates depending on the location of the insertion sites. Direct tandem duplications are lost by unequal crossing over, both mitotically and meiotically, at a frequency proportional to their sizes. These results show that most of the duplicated structures present an intrinsic level of instability. However, translocation within another chromosome significantly stabilizes a duplicated segment, increasing its chance to get fixed in a population even in the absence of any immediate selective advantage conferred by the duplicated genes.

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments

There is growing evidence that duplications have played a major role in eucaryotic genome evolution. Sequencing data revealed the presence of large duplicated regions in the genomes of many eucaryotic organisms, and comparative studies have suggested that duplication of large DNA segments has been a continuing process during evolution. However, little experimental data have been produced regarding this issue. Using a gene dosage assay for growth recovery in Saccharomyces cerevisiae, we demonstrate that a majority of the revertant strains (58%) resulted from the spontaneous duplication of large DNA segments, either intra- or interchromosomally, ranging from 41 to 655 kb in size. These events result in the concomitant duplication of dozens of genes and in some cases in the formation of chimeric open reading frames at the junction of the duplicated blocks. The types of sequences at the breakpoints as well as their superposition with the replication map suggest that spontaneous large segmental duplications result from replication accidents. Aneuploidization events or suppressor mutations that do not involve large-scale rearrangements accounted for the rest of the reversion events (in 26 and 16% of the strains, respectively).

Electrophoretic characterization of Aspergillus nidulans strains with chromosomal duplications

Pulsed-field gel electrophoresis was used to characterize strains of Aspergillus nidulans with a chromosomal duplication Dp(I-II). Morphologically deteriorated and improved variants of these strains were also analyzed. The electrophoretic karyotype demonstrated that in two duplicated strains (A and B) the 4.2 Mb band, which corresponds to chromosome II, was absent and a new band was observed. Hybridization studies using the uapA (chromosome I) and wA (chromosome II) genes demonstrated that the new band corresponded to chromosome II plus the duplicated segment of chromosome I. The size of the chromosomal duplication was approximately 1.0 Mb. Analysis of the chromosomal bands of a morphologically improved strain showed that the duplicated segment of chromosome I was completely lost. The morphologically deteriorated variants V9 and V17 had the same karyotype as the duplicated strains. However, the deteriorated variant V5 lost part of chromosome I and had a rearrangement involving chromosome V. This rearrangement may have resulted from the mutagenic treatment used to obtain the genetic markers. Pulsed-field gel electrophoresis was found to be an excellent tool for locating chromosomal rearrangements.

Wild chromosomal variants in Aspergillus nidulans

Pulsed-field gel electrophoresis and a chromosome-specific cosmid DNA library were used to determine the karyotypes of wild-type Aspergillus nidulans isolates from around the world. Overall, little structural variation was found, with a few major exceptions. One isolate possessed a non-essential B-chromosome of about 1.0 million base pairs (mb). Another isolate had undergone a non-reciprocal translocation of about 1.6 mb of chromosome VI onto chromosome VIII. Other than these chromosomal differences, these isolates appeared phenotypically normal. To analyze its effects on meiosis, the translocation isolate was outcrossed with another wild-type derivative that had a normal electrophoretic karyotype. This cross produced a range of phenotypes, including duplicated progeny that had a barren phenotype similar to that described for Neurospora partial disomics. The duplication was somewhat vegetatively unstable. This is the first association of sterility with chromosomal duplication in A. nidulans.

An intragenic map of the brlA locus of Aspergillus nidulans

We have constructed an intragenic map for the Aspergillus nidulans brlA gene, mutants in which are distinguishable by visual criteria only. Most of the leaky phenotype mutants map near the right (3') end. The gene shows distinct recombinational polarity consistent with recombination initiation at the promoter (centromere-proximal) end of the gene. brlA12 and brlA20 mutants gave abnormal DNA restriction patterns consistent with the III; VIII and VI; VIII translocations, respectively, determined by haploidization.

Genetic analysis of Aspergillus nidulans AmdS+ transformants

To correlate the genetic background of the Aspergillus nidulans amdS deletion strain MH1277 with the integrational behaviour of transforming vectors, classical genetic methods were used to construct AmdS- strains in which whole chromosomes had been exchanged with those of a master strain. Progeny strains were transformed to the AmdS+ phenotype with vector p3SR2. From Southern analysis it was concluded that transformants from all constructions contained tandemly repeated, multiple copy inserts of vector DNA as found for MH1277-derived AmdS+ transformants. AmdS+ transformants of MH1277 were analysed genetically to prove that the transformant phenotype is genome linked and that transformation by integration can take place on various chromosomes. In one case the AmdS+ property showed linkage to both chromosomes II and IV, due to a chromosomal translocation. Sexual analysis of two transformants with AmdS+ insertions on the same chromosome revealed a considerable instability of the AmdS+ phenotype in one of the strains upon selfing. Due to this instability no decisive answer could be given for the degree of linkage between the AmdS+ insertions in these transformants.

Spontaneous IR duplications generated at mitosis in Aspergillus nidulans: further evidence of a preferential site of transposed attachment

A radiation-induced translocation, T(IIR----IIIL), has been shown to be nonreciprocal and to have most of IIR, including its terminus, attached uninverted to the terminus of IIIL.--Progeny with the IIR segment in duplicate, obtained from crosses of T(IIR----IIIL) to strains with a standard genome, were unstable at mitosis; like earlier duplication strains, they suffered deletions from either duplicate segment. Frequent mitotic crossing over occurred between the duplicate IIR segments so that, following deletions, more than two classes of stable, balanced products arose from each heterozygous duplication strain.-- Spontaneous, mitotically arising duplications of the IR segment, bearing the rate-limiting adE20 allele, can be selected on adenine-free medium on which they emerge as vigorous sectors from the stunted adE20 colony. It was shown previously that most such duplications, when selected from a strain with standard genome, had the terminal IR segment attached to the end of IIR. Selection has now been made from an adE20 strain carrying T(IIR----IIIL), and seven of the 13 independent IR duplications were linked to the III-IIR translocation complex. In three strains analyzed further, the duplicate IR segments, which included the IR terminus, were attached uninverted to the terminus of IIR; the segments of IR were of approximately equal genetic length.--This supports earlier suggestions that there is a preferential site for the initiation of IR duplications and a preferential site, the IIR terminus, for their attachment.

Two-way selection of mutants and revertants to chloroneb resistance in Aspergillus nidulans

5 mutants of Aspergillus nidulans, selected for resistance to chloroneb, were also partially dependent on it. The resistance of these mutants to chloroneb was about 20-150 times higher than that of the original strain. The resistance marker was due to a mutation in a single gene, located in linkage group III, and behaved as a recessive character. This genetic marker was distal in relation to galAl with a recombination frequency of about 30-35%. The different levels of resistance were attributed to mutations at different sites in the same locus. Both stable and unstable sectors were obtained from resistant strains inoculated on chloroneb-free medium. The emergence of stable sectors was due to back mutation, suppressor mutation or another mutation, which allows growth to the full extent in the absence of the drug. The unstable sectors showed better growth when compared with the resistant strain, kept their resistance and produced both resistant and non-resistant secondary sectors. This procedure of 2-way selection of mutants and revertants to chloroneb resistance could be useful for studying forward and back mutation in A. nidulans.

Reversion in variants from a duplication strain of Aspergillus nidulans

Strains of Aspergillus nidulans with a chromosome segment in duplicate, one in normal position and one translocated to another chromosome, are unstable at mitosis. In addition to variants which result from deletions in either of the duplicate segments, which usually have improved morphology, they produce variants with deteriorated morphology. Three deteriorated variants reverted frequently to parental type morphology, both spontaneously and after ultra-violet treatment. Of six reversions analysed genetically, five were due to suppressors and one was probably due to back mutation. The suppressors segregated as single genes and were not linked to the mutation which they suppress. The instability of these so-called "deteriorate"variants is discussed in relation to mitotic instability phenomena in A. nidulans.

The effects of coumarin on the frequency of deletions in a duplication strain of Aspergillus nidulans

Strains of A. nidulans with a chromosome segment in duplicate show instability resulting from deletions in either of the duplicate segments. In Dp (I, II) strains, with the terminal segment of IR attached terminally to IIR, spontaneous deletions occur most frequently, though not exclusively, from the translocated segment. Coumarin, at concentrations which did not affect viability viability or growth rate, enhanced the instability of Dp (I, II) strains by selectively increasing only the deletion class of highest spontaneous frequency. This selective action is interpreted tentatively as due to inhibition of the repair of a particular class of DNA lesion occurring spontaneously in the attachment region of Dp (I, II) strains.

Effects of ethidium bromide in diploid and duplication strains of Aspergillus nidulans

Unstable duplication and diploid strains of Aspergillus nidulans were treated with ethidium bromide, and it was shown that this drug reduces the number of sectors produced by such strains. The mechanisms which could be responsible for the partial stabilization of the strains are discussed and it is suggested that a similar mechanism is responsible for the production of sectors in both strains. It is also suggested that ethidium bromide could be useful for the reduction of instability of industrial strains.

The genetic instability and mutagenic interaction of chromosomal duplications present together in haploid strains of Aspergillus nidulans

Previous work has shown that strains of Aspergillus nidulans with a chromosome segment in duplicate (one in normal position, one translocated to another chromosome) are unstable. Deletions occur from either duplicate segment. The present work has shown that when a chromosome I duplication and a chromosome III duplication are together in a haploid, deletions from the intact III duplication generally precede deletions from particular sections of the I duplication. Furthermore, the III duplication can enhance to some (but not major) extent the frequency of deletions from the I duplication. After the III duplication becomes reduced in size as a result of the loss of chromosomal material from the translocated duplicate III segment, such a reduced III duplication can greatly enhance the frequency of deletions from the I duplication. In other words, a III duplication of reduced size can promote far more deletions from the I duplication than the intact III duplication. The major increase in the deletional instability of the I duplication as promoted by the reduced III duplication is confined to the translocated duplicate I segment. The reduced III duplication can induce deletions from a section of the translocated duplicate I segment in accord with a temporal programme, and it appears that a particular region of the I duplication is far more under the mutagenic influence of the reduced III duplication than another region. Moreover, there is indication that there is a differential effect of two generally different genetic backgrounds on the susceptibility of duplication-regions to deletion. Possible mechanisms involved in such chromosomal instability are proposed. A manner in which genetic instability may be related to development is also proposed.

The effects of temperature on genetic instability in Aspergillus nidulans

Previous work has shown that strains of Aspergillus nidulans with a chromosome segment in duplicate (one in normal position, one translocated to another chromosome) are unstable. Deletions occur from either duplicate segment. The present work has shown that most deletions occur from the translocated duplicate segment. Furthermore, it has been found that the overall frequency of deletions from a duplication is dependent upon the temperature of growth. The overall frequency of deletions from a chromosome III duplication is greatly enhanced by low temperatures, while the overall frequency of deletions from a chromosome I duplication is markedly enhanced by high temperatures. A temperature of 39.5 degrees C appears to enhance to overall frequency of deletions from the I duplication to the greatest extent. With regard to the non-translocated duplicate I segment, an increase in temperature progressively enhances the frequency of those deletions to which it is subject to far more deletions during a particular period of growth than during any other period, and at 42 degrees C, a section of the III duplication is subject to far more deletions during a given period of growth than during any other period. Comparisons with other cases of genetic instability are made and common underlying connections are proposed.

Genetic control of chromosome instability in Aspergillus nidulans as a mean for gene amplification in eukaryotic microorganisms

A haploid strain of Aspergillus nidulans carrying I-II duplication homozygous for the leaky mutation adE20 shows impreved growth on minimal medium. The duplication, though more stable than disomics, still shows instability. Several methods were used for detecting genetic control of improved stability. (a) visual selection, using a duplicated strain which is very unstable due to UV sensitivity, (adE20, biAl/dp yA2; uvsB). One stable strain showed a deletion (or a lethal mutation?) DISTAL TO BIA on the segment at the original position (on chromosome I). This deletion reduces crossing over frequency between the two homologous segments. As the deletion of the non-translocated segment (yelow sectors) must be preceded by crossing over, the above reduces the frequency of yellow sectors. A deletion of the translocated segment (green sectors) results in non-viability due to the deletion, and such sectors do not appear. The net result is a stable duplication involving only 12 C.O. units carrying the gene in concern. (b) Suppressors of UV sensitivity (su-uvsB) were attempted using the above uvs duplicated strain. Phenotypic revertants were easily obtained, but all were back mutations at the uvsB locus. (c) Mutations for UV resistance higher than that of the wild type were not obtained, in spite of the strong selective pressure inserted. (d) Recombination deficient mutations (rec), six altogether, all uvs+, did not have any effect on stability.

Escape from mating-type incompatibility in bisexual (A + a) Neurospora heterokaryons

In Neurospora crassa, strains of opposite mating type generally do not form stable heterokaryons because the mating type locus acts as a heterokaryon incompatibility locus. However, when one A and one a strain, having complementing auxotrophic mutants, are placed together on minimal medium, growth may occur, although the growth is generally slow. In this study, escape from such slow growth to that at a wild type or near-wild type rate was observed. The escape cultures are stable heterokaryons, mostly having lost the mating type allele function from one component nucleus, so that the nuclear types are heterokaryon compatible. Either A or a mating type can be lost. This loss of function has been attributed to deletion since only one nuclear type could be recovered in all heterokaryons except one, but deletion spanning adjacent loci has been directly demonstrated in a minority of cases. Alternatively when one component strain is tol and the other tol+ (tol being a recessive mutant suppressing the heterokaryon incompatibility associated with mating type), escape may occur by the deletion or mutation of tol+, also resulting in heterokaryon compatibility. An induction mechanism for escape is speculated upon.

Altered instability due to genetic changes in a duplication strain of Aspergillus nidulans

Strains ofAspergillus nidulanswith a duplicate segment are mitotically unstable; they produce phenotypically improved variants following deletions in either duplicate segment, and morphologically deteriorated types. The number of variants produced is characteristic of each duplication strain under the same conditions. After ultraviolet treatment two variants, one more stable and the other less stable than the original strain, were selected. Genetic analysis showed that the increased instability in the less stable variant was due to a translocation involving linkage groups V and VIII. The increased stability of the more stable variant was due to a recessive factor (stf–1) located in linkage group VIII. In the homozygous condition this factor also reduces the number of sectors in a diploid strain. The possible genetic mechanisms explaining the instability alterations are discussed.

A simple and rapid technique for obtaining a high proportion of hybrid cleistothecia in Aspergillus nidulans

A technique is reported for crossing strains of Aspergillus nidulans which produces hybrid cleistothecia in 7 days. The method depends on the partial inhibition of cleistothecium formation of auxotrophic mutants by growth-factor limitation. Cleistothecia form at the junction of two strains inoculated on to complete medium. The method has a number of advantages over standard techniques.

A variegated position effect in Aspergillus nidulans

In mutants at the ‘bristle’ locus ofAspergillus nidulansthe conidiophore remains as a stiff hypha rather than developing a vesicle, sterigmata and conidia. ThebrlA12 allele of this locus has a variegated phenotype, and genetic analysis has shown that this is associated with a translocation which has a breakpoint in the map interval adjacent to thebristlelocus.

The mutant phenotype is partially repaired on high-salt medium at low pH, and can also be repaired by suppressors, one of which has been mapped at a locus unlinked tobrlA12.

The mutant provides proof that variegation is due to instability of gene expression and not to mutability sincebrlA12 is genetically stable and can be propagated from either conidia or sterile conidiophores, the structures formed at the two extremes of variegation, and the resulting colonies in both cases are identical to the original strain.

It has been shown by mitotic recombination that the translocation associated with the variegated mutant is a ‘simple translocation’ in which the distal half of linkage group VIII is attached to the end of linkage group III. This terminal attachment site does not appear to be damaged in any genetically detectable way.

Mitotic non-conformity in Aspergillus: successive and transposable genetic changes

Strains ofAspergillus nidulanswith, a duplicate chromosome segment are mitotically unstable; in addition to phenotypically improved variants, arising following deletions in either duplicate segment, they give morphologically deteriorated types, some with, enhanced stability. In one isolate, deterioration and increased instability were determined by mutation in a duplicate segment; a more stable derivative no longer had this mutation but had one in another linkage group. Another variant, too unstable for analysis, gave derivatives whose single, new mutations were in different linkage groups. It is proposed that deterioration and increased instability result from tandem duplications on either duplicate segment; transposition of these to non-duplicated regions reduces instability. Another 17 variants had a single new mutation each; mutations, possibly clustered, occurred in all linkage groups. In these strains perhaps transposition preceded analysis. Deteriorated variants gave lineages of types with morphological changes caused by further, superimposed mutations. This continued instability is explained as interaction, in fidelity of replication, of non-homologous chromosome segments.

Instability inA. nidulansstems from chromosome imbalance. As imbalance is known or suspected in other cases of instability it may be possible to show common mechanisms for apparently diverse phenomena.

Mitotic non-conformity in Aspergillus nidulans: the production of hypodiploid and hypohaploid nuclei

Strains ofAspergillus nidulanswith a chromosome segment additional to the normal complement are vegetatively unstable. Previous work suggested that the deletions occurring at mitosis were confined to the unbalanced segments. It has been shown now that deletions, while probably always involving a duplicate segment, may extend beyond it to produce hypohaploids and hypodiploids, respectively, from unbalanced haploid and unbalanced diploid parents.

Hypoploids have been proposed tentatively as an explanation for some cases of phenotypic variegation; on this basis it is possible to account for some of the diverse phenomena shown by, for example, position-effect variegation.

A system generating spontaneous intrachromosomal changes at mitosis in Aspergillus nidulans

Previous studies had shown that haploid strains ofAspergillus nidulanswhich have a chromosome segment in duplicate are unstable at mitosis. Through the study of various haploid and diploid strains, with and without translocations and with balanced and unbalanced genomes, it has been shown: (1) that imbalance of chromosome segments is responsible for instability, and (2) that the chromosomal deletions produced are confined solely or largely to the segments which provoke instability.

The term ‘mitotic non-conformity’ has been proposed for this instability phenomenon. An explanation for it has been sought in terms of attachment sites, limited in number and specific for chromosome segments, at which replication is initiated.

Analysis of the genetic instability induced by nitrous acid in Schizosaccharomyces pombe

A pedigree analysis of several cell-colony generations following a mutagenic treatment with nitrous acid has shown that in S. pombe a genetic instability is produced that replicates several times and produces a mutation in independent lines.

It has been shown that the mutants isolated in the progeny of a mosaic colony all contain a genetic alteration that cannot be resolved by genetic analysis and therefore the mutations have occurred at the same genetic site. This finding is confirmed by interallelic complementation and phenotypic analyses.

Chromosome instability related to gene suppression in Aspergillus nidulans

A complicated system of chromosome instability related to gene suppression has been analysed. In addition, unstable genetic events analogous to those previously described inA. nidulansand in other organisms have been detected and one type of unstable variant recovered may be determined by V-type position effect. Furthermore, the selective systems used, clearly offer scope for analysis of genetic instability in general.