Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)

Genome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of the CesA region in two cotton genomes that diverged 5–10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A ( AdhA ) from four cotton genomes: the two co-resident genomes (A_T and D_T) of the allotetraploid, Gossypium hirsutum , as well as the model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). In contrast to earlier work, evolution in the AdhA region reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of 'genomic downsizing' in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post-polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.     

Salt‐tolerance diversity in diploid and polyploid cotton (Gossypium) species

The development of salt‐tolerant genotypes is pivotal for the effective utilization of salinized land and to increase global crop productivity. Several cotton species comprise the most important source of textile fibers globally, and these are increasingly grown on marginal or increasingly saline agroecosystems. The allopolyploid cotton species also provide a model system for polyploid research, of relevance here because polyploidy was suggested to be associated with increased adaptation to stress. To evaluate the genetic variation of salt tolerance among cotton species, 17 diverse accessions of allopolyploid (AD‐genome) and diploid (A‐ and D‐genome) Gossypium were evaluated for a total of 29 morphological and physiological traits associated with salt tolerance. For most morphological and physiological traits, cotton accessions showed highly variable responses to 2 weeks of exposure to moderate (50 mm NaCl) and high (100 mm NaCl) hydroponic salinity treatments. Our results showed that the most salt‐tolerant species were the allopolyploid Gossypium mustelinum from north‐east Brazil, the D‐genome diploid Gossypium klotzschianum from the Galapagos Islands, followed by the A‐genome diploids of Africa and Asia. Generally, A‐genome accessions outperformed D‐genome cottons under salinity conditions. Allopolyploid accessions from either diploid genomic group did not show significant differences in salt tolerance, but they were more similar to one of the two progenitor lineages. Our findings demonstrate that allopolyploidy in itself need not be associated with increased salinity stress tolerance and provide information for using the secondary Gossypium gene pool to breed for improved salt tolerance.     

Difference between diploid and aneuploid Chinese hamster cells in replication at mid-S-phase

Following partial synchronization of the heteroploid Chinese hamster cell line V-79 and of normal diploid lung fibroblasts of the Chinese hamster in culture, their DNA replication during S-phase was compared by means of a BrdU-incorporation/thymidine pulse technique and Hoechst-Giemsa differential staining of metaphase chromosomes. This comparison indirectly shows the S-phase of the heteroploid cells of V-79 to be 2 h shorter than the diploid cell S-phase. When the thymidine pulse is applied to diploid lung fibroblasts at mid-S-phase, differential staining colours metaphase chromosomes a pale blue. Performing the corresponding experiment with V-79 cells, neither a pale blue nor dark red staining is obtained, but rather an intermediate shade, showing prominently dark staining regions in parts. The pause in DNA synthesis observed at mid-S-phase of the diploid Chinese hamster lung fibroblasts seems to be omitted at mid-S-phase of the V-79 cells.     

Cell cycles in human diploid and aneuploid strains

Summary Autoradiographic investigation of the cell cycle of 12 diploid and 12 abnormal human fibroblast strains was carried out. Two cell strains (trisomy 7 and monosomy 21) derived from spontaneous abortuses showed prolongation of the G₂ period accompanied by the shortening of the S period. Other cytogenetically abnormal embryonic strains (trisomy 9, 14 and triploidy) did not deviate from the diploid pattern. Three cell strains (LHC-1-70, LHC-6-70, LHC-411) derived from the patients with karyotypes 47,XXX, 47,XY,+18 and 46,XX,5p—respectivly had embryonic types of proliferation with a short G₂ period. In two other strains from the patients with Down's syndrom the G₂ period was prolonged. There was no statistically significant difference in the parameters of the cell cycle between the control and the strains derived from a patient with Klinefelter syndrom and from a male patient with karyotype 46,XX. The modificatory effect of the chromosomal abnormalities on the parameters of cell cycle is discussed.

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Zusammenfassung Der Zellcyclus von 12 normal diploiden und 12 abnormen menschlichen Fibroblasten-Zellinien wurde untersucht. Zwei Zellinien (Trisomie 7 und Monosomie 21) zeigten eine Verlängerung der G₂-Phase und eine Verkürzung der S-Phase. Zellinien (Trisomie 9, 14 und Triploidie) wichen nicht von der Norm ab. Drei Zellinien (47,XXX; 47,XY,+18; 46,XX,5p-) zeigten eine Verkürzung von G₂. G₂ war dagegen verlängert bei zwei Zellinien von Down-Syndrom. Keine Abweichung fand sich bei einem Klinefelter-Patienten und einem männlichen Probanden mit 46,XX.

     

Rapid structural and epigenetic changes in polyploid and aneuploid genomes

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes. BioEssays 21:761–767, 1999. © 1999 John Wiley & Sons, Inc.     

Sequence characterization of microsatellites in diploid and polyploid Ipomoea

 The objectives of the present study were to evaluate the inheritance and nucleotide sequence profiles of microsatellite genetic markers in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] and its putative tetraploid and diploid ancestors, and to test possible microsatellite mutation mechanisms in polyploids by direct sequencing of alleles. Sixty three microsatellite loci were isolated from genomic libraries of I. batatas and sequenced. PCR primers were designed and used to characterize microsatellite loci in two hexaploid I. batatas populations, a tetraploid Ipomoea trifida population, and a diploid I. trifida population. Nine out of the sixty three primer pairs tested yielded a clearly discernible, heritable banding pattern; five showed Mendelian segregation. All other primer pairs produced either smeared banding patterns, which could not be scored, or no bands at all in I. batatas. All of the primers which produced discernible banding patterns from I. batatas also amplified products of similar size in tetraploid and diploid I. trifida accessions. The sequence analysis of several alleles in the three species showed differences due to mutations in the repeat regions consistent with small differences in the repeat number. However, in some cases insertions/deletions and base substitutions in the microsatellite flanking regions were responsible for polymorphisms in both polyploid and diploid species. These results provide strong empirical evidence that complex genetic mechanisms are responsible for SSR allelic variation in Ipomoea. Four I. batatas microsatellite loci showed polysomic segregation fitting tetraploid segregation ratios. To our knowledge this is the first report of segregation ratios for microsatellites markers in polyploids. Received: 4 January 1999 / Accepted: 4 January 1999     

Survival of aneuploid, micronucleated and/or polyploid cells: crosstalk between ploidy control and apoptosis

Microtubule inhibitors are known to block the cell cycle at M-phase, by damaging the mitotic spindle. However, under certain circumstances, cells can escape these effects and become aneuploid, polyploid and/or micronucleated. It is well known that aneuploidy can have adverse effects on human health such as pregnancy wastage, birth defects and the development of human tumours. The present paper aims at reviewing the data our laboratory has accumulated during the last years about the relation between aneuploidy/polyploidy/presence of micronuclei and the induction of apoptosis in human cells after in vitro exposure to the microtubule inhibitor nocodazole. Exposure to high doses of nocodazole results in polyploidy due to mitotic slippage in the absence of a functional spindle. Depending on their p53-status polyploid cells may eventually arrest, die or continue cycling. In these experimental conditions, our data showed that polyploidy does not constitute a strong apoptotic signal. In case of exposure to low concentrations of nocodazole, microtubule depolymerization is disturbed resulting in a spindle with damaged microtubules. This can give rise to chromosome loss and non-disjunction. Our data showed that in particular micronucleated cells, originating from chromosome loss can be eliminated by apoptosis. In addition, nocodazole-induced apoptosis involves the apical caspase-8 and -9 and the effector caspase-3. We show evidence that caspase-3, in addition to its function in apoptosis, plays a role in the formation of micronuclei.     

Radiation-induced aberration in aneuploid vs. diploid swine leukocytes

Swine leukocytes were cultured for 48 h after receiving γ-ray exposures up to 400 R. Cells with one or two less than the diploid number of centromeres consistently contained more chromosome deletions than did diploid cells. This effect was not evident for dicentric and ring aberrations. Both aneuploid frequencies and the proportion of aberrations in aneuploid cells increased in irradiated samples but showed no dose-response relationship.     

The tumorigenicity of diploid and aneuploid human pluripotent stem cells

Human embryonic stem cells (HESCs) and induced pluripotent stem cells (HiPSCs) offer an immense potential as a source of cells for regenerative medicine. However, the ability of undifferentiated HESCs to produce tumors in vivo presents a major obstacle for the translation of this potential into clinical reality. Therefore, characterizing the nature of HESC-derived tumors, especially their malignant potential, is extremely important in order to evaluate the risk involved in their clinical use. Here we review recent observations on the tumorigenicity of human pluripotent stem cells. We argue that diploid, early passage, HESCs produce benign teratomas without undergoing genetic modifications. Conversely, HESCs that acquired genetic or epigenetic changes upon adaptation to in vitro culture can produce malignant teratocarcinomas. We discuss the molecular mechanisms of HESC tumorigenicity and suggest approaches to prevent tumor formation from these cells. We also discuss the differences in the tumorigenicity between mouse embryonic stem cells (MESCs) and HESCs, and suggest methodologies that may help to identify cellular markers for culture adapted HESCs.     

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.     

NADP-dependent aromatic alcohol dehydrogenase in polyploid wheats and their diploid relatives. On the origin and phylogeny of polyploid wheats

Summary The three major isoenzymes of the NADP-dependent aromatic alcohol dehydrogenase (ADH-B), distinguished in polyploid wheats by means of polyacrylamide gel electrophoresis, are shown to be coded by homoeoalleles of the locus Adh-2 on short arms of chromosomes of the fifth homoeologous group. Essentially codominant expression of the Adh-2 homoeolleles of composite genomes was observed in young seedlings of hexaploid wheats (T. aestivum s.l.) and tetraploid wheats of the emmer group (T. turgidum s.l.), whereas only the isoenzyme characteristic of the A genome is present in the seedlings of the timopheevii-group tetraploids (T. timopheevii s.str. and T. araraticum).The slowest-moving B³ isoenzyme of polyploid wheats, coded by the homoeoallele of the B genome, is characteristic of the diploid species Aegilops speltoides S.l., including both its awned and awnless forms, but was not encountered in Ae. bicornis, Ae. sharonensis and Ae. longissima. The last two diploids, as well as Ae. tauschii, Ae. caudata, Triticum monococcum s.str., T. boeoticum s.l. (incl. T. thaoudar) and T. urartu all shared a common isoenzyme coinciding electrophoretically with the band B² controlled by the A and D genome homoeoalleles in polyploid wheats. Ae. bicomis is characterized by the slowest isoenzyme, B⁴, not found in wheats and in the other diploid Aegilops species studied.Two electrophoretic variants of ADH-B, B¹ and B², considered to be alloenzymes of the A genome homoeoallele, were observed in T. dicoccoides, T. dicoccon, T. turgidum. s.str. and T. spelta, whereas B² was characteristic of T. timopheevii s.l. and only B¹ was found in the remaining taxa of polyploid wheats. The isoenzyme B¹, not encountered among diploid species, is considered to be a mutational derivative which arose on the tetraploid level from its more ancestral form B² characteristic of diploid wheats.The implication of the ADH-B isoenzyme data to the problems of wheat phylogeny and gene evolution is discussed.     

Cytological studies on diploid and polyploid taxa of the genus Pennisetum Rich

The cytology of thirteen taxa and two hybrids in the genus Pennisetum indicated the distribution of the taxa among the four basic chromosome numbers 5, 7, 8 and 9. The diploid nature of P. ramosum and P. typhoides and the genomic allotetraploid status of P. purpureum was further confirmed. P. massaicum (2n=32), P. orientale (2n=36) and P. subangustum (2n=36) suggested probable autotetraploid nature and the three hexaploids (2n=54) investigated (P. polystachyon, P. longistylis and P. squamulatum) revealed allohexaploid constitution. The natural triploid, P. ruppellii (2n=27) and pentaploid P. villosum (2n=45) were found to be apomicts and they were allotriploid and allopentaploid respectively. The tetraploid-hexaploid complex of P. pedicellatum showed them to be cytotypes only. The cytogenetical behaviour of the hybrid, P. typhoides x P. purpureum with 2n=21 and the trispecies hybrid (P. typhoides x P. purpureum) x P. squamulatum with 2n=48 brought out the homology within the genomes of x=7 and x=9 and also between the genomes with x=7 and x=9. The significance of the inter- and intragenomic chromosome pairing had been brought out from the interspecific hybrids and the natural allotriploid and allopentaploid species having one genome in the haploid condition.The morphological sections of this genus did not correspond with the cytological groups. A high degree of evolutionary specialization was evident in species of the section Gymnothrix. A complete series of polyploids and high degree of heterogeneity from the morphological point of view was brought out in species with x=9.     

Clone heterogeneity in diploid and aneuploid breast carcinomas as detected by FISH

We investigated the relationship between DNA ploidy and alterations in chromosomes 1, 8, 12, 16, 17, and 18 in 63 breast carcinoma samples by static cytofluorometry and fluorescence in situ hybridization. Thirty specimens were diploid and 33 were aneuploid. In aneuploid samples, the DNA index value ranged from 1.3 to 3.1, with a main peak near tetraploid values. Diploid clones were present in 21 of 33 aneuploid specimens. Fluorescence in situ hybridization analysis showed a heterogeneous degree of alterations in diploid specimens: one sample was normal, 16 samples had one to three chromosome alterations involving mostly chromosomes 1, 16, and 17, and 13 samples an even higher degree of alterations. The 33 aneuploid specimens showed a very high number of signals (four, five, or more). All the investigated chromosomes were affected in 23 of 33 specimens. Alterations in chromosomes 1 and 17 were detected to a similar percentage in diploid and aneuploid samples, whereas chromosome 16 monosomy was more frequent in diploid samples. Overrepresentation of chromosomes 8, 12, 16, and 18 was significantly higher in aneuploid than in diploid samples. Based on these results, we suggest that diploid and aneuploid breast carcinomas are genetically related. Chromosome 1 and 17 alterations and chromosome 16 monosomy are early changes. Allelic and chromosomal accumulations occur during progression of breast carcinoma by different mechanisms. The high clone heterogeneity found in 17 of 33 aneuploid samples could not be completely explained by endoreduplication and led to the suggestion that chromosomal instability concurs with aneuploidy development. This different evolutionary pathway might be clinically relevant because clone heterogeneity might cause metastasis development and resistance to therapy.