Role In Chromosome Evolution Research Articles

Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.

BackgroundThe development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.ResultsWe present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.ConclusionsTested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ∼1 GB, which makes Smash++ feasible to run on present-day standard computers.

Frequent variations in tandem repeats pSc200 and pSc119.2 cause rapid chromosome evolution of open-pollinated rye

Variation in heterochromatin is thought to play an important role in chromosome evolution in cereal rye (Secale cereale). This theory has been based on only limited numbers of sampled individuals, as it is difficult to handle large numbers in detailed cytogenetic analyses. In this study, we analyzed a relatively large number of individuals comprising 300 plants from six open-pollinated rye cultivars using oligonucleotides TAMRA-oligo-6 and FAM-pSc119.2-1 that represent tandem repeats of pSc200 and pSc119.2, respectively. Seventy-three types of heterochromatin blocks were identified on all seven chromosomes: 43 from pSc119.2 and 30 from pSc200. Eight block types were fully conserved, and variants in 65 (89.04%) had frequencies ranging from 0.17 to 49.67% and an average of 14.47%. Block 6R-g3 (49.67%) had the highest frequency of variation. Higher average frequencies of variation in block types were revealed by pSc200 (19.33%) than by pSc119.2 (11.08%). A total of 322 polymorphic chromosomes (combinations of different block types) were identified, including 79 major types with frequencies higher than expected, including 14 that were fivefold higher. Six preferentially transmitted chromosomes were confirmed by karyotype analysis in 40 wheat-rye F1 plants. Among the 300 plants investigated, there were 63.00 to 86.66% heterozygosity and 43.66 to 90.32% heterogeneity for each chromosome. Results from this research confirmed rapid chromosome change and high levels of chromosome diversity in heterochromatin blocks in rye.

Structure, behaviour and repetitive DNA of B-chromosomes in Cestrum nocturnum (Solanaceae)

The Cestrum genus is karyotypically exceptional in Solanaceae. It is characterised by a basic number x = 8, a large chromosomal and genomic size, complex heterochromatin patterns, B-chromosomes (Bs) with particular heterochromatin and distribution of 18–5.8–26S and 5S rDNA. Cestrum nocturnum L. has a diploid number of 2n = 16 plus a variable number of B-chromosomes. The aims of work was to analyse their numerical variation, structure and behaviour of C. nocturnum B-chromosomes by classical and molecular cytogenetics. The individuals analysed had 2n = 16 + 0−13 B-chromosomes. All B-chromosomes were metacentric and smaller than A-chromosomes. The number of B-chromosomes showed a great variability between and within individuals, thereby denoting the occurrence of events that promote mitotic and meiotic instability. Cytogenetic techniques made it possible to observe that B-chromosomes are rich in heterochromatin, probably with AT- and GC-rich regions. In addition, molecular techniques allowed to detect homologous sequences of transposable element conserved domains of Ty1-Copia and Ty3-Gypsy superfamilies. These sequences were located by FISH in all B-chromosomes and some A-chromosomes. Our results showed that repetitive DNA could play an important role in chromosomal evolution as well as in the stability of B-chromosomes in C. nocturnum.

Satellite DNA: An Evolving Topic.

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

Karyotype Evolution in the Horseshoe Bat Rhinolophus sedulus by Whole-Arm Reciprocal Translocation (WART)

Robertsonian (centric) fusion or fission is one of the predominant modes of chromosomal rearrangement in karyotype evolution among mammals. However, in karyotypes composed of only bi-armed chromosomes, creation of new chromosomal arm combinations in one step is possible only via whole-arm reciprocal translocation (WART). Although this type of rearrangement has often been proposed to play an important role in chromosomal evolution, direct observations of WARTs remained rare, and, in most cases, were found in hybrids of chromosomal races in the genera Mus and Sorex. For the first time, we present the karyotype of the horseshoe bat species Rhinolophus sedulus (2n = 28, FNa = 52), where a WART between 2 metacentric autosomes was detected by G-banding and confirmed by FISH with painting probes of the vespertilionid bat Myotis myotis. Among the 6 specimens analyzed, 2 showed the heterozygous condition of the WART, 1 showed the presumed ancestral, and 3 specimens showed the derived homozygous state. As the existence of a hybrid zone at the sampling locality is thought to be rather improbable, the WART may indicate ongoing karyotype evolution in this taxon.

Chromosomal Replication Dynamics and Interaction with the β Sliding Clamp Determine Orientation of Bacterial Transposable Elements

Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact with the host. Here, we report a survey of the orientation patterns of ISs in bacterial chromosomes with the objective of gaining insight into the interplay between ISs and host chromosomal functions. We find that a significant fraction of IS families present a consistent and family-specific orientation bias with respect to chromosomal DNA replication, especially in Firmicutes. Additionally, we find that the transposases of up to nine different IS families with different transposition pathways interact with the β sliding clamp, an essential replication factor, suggesting that this is a widespread mechanism of interaction with the host. Although we find evidence that the interaction with the β sliding clamp is common to all bacterial phyla, it also could explain the observed strong orientation bias found in Firmicutes, because in this group β is asymmetrically distributed during synthesis of the leading or lagging strands. Besides the interaction with the β sliding clamp, other asymmetries also play a role in the biased orientation of some IS families. The utilization of the highly conserved replication sliding clamps suggests a mechanism for host regulation of IS proliferation and also a universal platform for IS dispersal and transmission within bacterial populations and among phylogenetically distant species.

Molecular phylogeny and chromosome evolution among the creeping herbaceous Oxalis species of sections Corniculatae and Ripariae (Oxalidaceae)

Oxalis sections Corniculatae DC. and Ripariae Lourteig are composed mainly of creeping herbs. They not only share strong morphological similarities, such as the presence of a reptant stem but also some cytogenetic characteristics. Several species in section Corniculatae share a base chromosome number x=5 with species in section Ripariae, while other species in the former have a x=6. We used a molecular and cytogenetic approach to determine the phylogenetic relationships, test the previous taxonomic classification and study the genome rearrangements that led to the differences in chromosome size and basic chromosome number between both sections. Phylogenetic relationships were inferred based on DNA sequences from chloroplast and nuclear ribosomal ITS. The molecular phylogenetic analyses found that neither of the sections are monophyletic, but do support two clades. The first group contains diploid species with x=5, large chromosomes and high DNA content and the second diploid and polyploidy species with x=6, small chromosomes and low DNA content. The x=5 clade comprises species of both sections, while the x=6 clade was formed mainly by section Corniculatae species and O. serpens from section Ripariae. Our results suggest that x=5 and high DNA content are derived conditions, which may have resulted from descendent disploidy and proliferation of transposable elements. Thus, cytogenetic data superimposed on the phylogeny have shown two different modes of chromosome evolution in both lineages: (1) chromosome rearrangements and increase in genome size in the x=5 lineage and (2) polyploidy playing the main role in chromosome evolution among species in the x=6 species. A taxonomic revision for the two sections is suggested.

Chromosome number of Orthophytum species (Bromeliaceae)

The genus Orthophytum Beer comprises 53 species, all narrow endemics to south-eastern and north-eastern Brazil. In this study we present meiotic and mitotic chromosome numbers of 12 species of this important genus in Bromeliaceae. For six of these taxa we are reporting the first cytogenetic study. Orthophytum albopictum, O. amoenum and O. burle-marxii presented 2n = 100 chromosomes and O. hatschbachii, O. mucugense, O. vagans, O. supthutii, O. zanonii and O. ophiuroides showed 2n = 50 chromosomes. These results are consistent with the proposed basic number of x = 25 for Bromeliaceae family. In the genus Orthophytum, polyploidy seems to play an important role in chromosome evolution associated with habitat differentiation among diploid and polyploid species.

High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

BackgroundComparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs) have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse.ResultsThe bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes.ConclusionAnalysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

Identification of a 3.0-kb Major Recombination Hotspot in Patients with Sotos Syndrome Who Carry a Common 1.9-Mb Microdeletion

Sotos syndrome (SoS) is a congenital dysmorphic disorder characterized by overgrowth in childhood, distinctive craniofacial features, and mental retardation. Haploinsufficiency of the NSD1 gene owing to either intragenic mutations or microdeletions is known to be the major cause of SoS. The common approximately 2.2-Mb microdeletion encompasses the whole NSD1 gene and neighboring genes and is flanked by low-copy repeats (LCRs). Here, we report the identification of a 3.0-kb major recombination hotspot within these LCRs, in which we mapped deletion breakpoints in 78.7% (37/47) of patients with SoS who carry the common microdeletion. The deletion size was subsequently refined to 1.9 Mb. Sequencing of breakpoint fragments from all 37 patients revealed junctions between a segment of the proximal LCR (PLCR-B) and the corresponding region of the distal LCR (DLCR-2B). PLCR-B and DLCR-2B are the only directly oriented regions, whereas the remaining regions of the PLCR and DLCR are in inverted orientation. The PLCR, with a size of 394.0 kb, and the DLCR, with a size of of 429.8 kb, showed high overall homology (approximately 98.5%), with an increased sequence similarity (approximately 99.4%) within the 3.0-kb breakpoint cluster. Several recombination-associated motifs were identified in the hotspot and/or its vicinity. Interestingly, a 10-fold average increase of a translin motif, as compared with the normal distribution within the LCRs, was recognized. Furthermore, a heterozygous inversion of the interval between the LCRs was detected in all fathers of the children carrying a deletion in the paternally derived chromosome. The functional significance of these findings remains to be elucidated. Segmental duplications of the primate genome play a major role in chromosomal evolution. Evolutionary study showed that the duplication of the SoS LCRs occurred 23.3-47.6 million years ago, before the divergence of Old World monkeys.

Distance from the Chromosome End Determines the Efficiency of Double Strand Break Repair in Subtelomeres of Haploid Yeast

Double strand break (DSB) repair plays an important role in chromosome evolution. We have investigated the fate of DSBs as a function of their location along the yeast chromosome XI, in a system where no conventional homologous recombination can occur. We report that the relative frequency of non-homologous endjoining (NHEJ), which is the exclusive mode of DSB repair in the internal chromosomal portion, decreases gradually towards the telomere, keeping the absolute frequency nearly constant, and that other repair mechanisms, which generally involve the loss of the distal chromosomal fragment, appear in subtelomeric regions. Distance of the DSB from chromosome ends plays a critical role in the global frequency of these repair mechanisms. Direct telomere additions are rare, and other events such as break-induced replication, plasmid incorporation, and gene conversion, involve acquisition of heterologous sequences. Therefore, in subtelomeric regions, cell survival to DSBs is higher and alternative modes of repair allow new genomic combinations to be generated. Furthermore, subtelomeric rearrangements depend on the recombination process, which, unexpectedly, also promotes the joining of heterologous sequences. Finally, we report that the Rad52 protein increases the efficiency of NHEJ.

Metaphase Karyotypes of Fruit Flies of Thailand. V. Cytotaxonomy of Ten Additional New Species of the Bactrocera dorsalis Complex.

Analysis of mitotic chromosomes, with special emphasis on the amount and distribution of constitutive heterochromatin, from larval samples of Thai populations of flies in the Bactrocera dorsalis complex has revealed 10 distinctive forms of metaphase karyotypes. This cytological evidence coupled with morphological observations of adults and host relationships with different host plant species have suggested the existence of 10 new cytotaxonomic species provisionally named species Q-Z belonging to the B. dorsalis complex. Metaphase karyotypes of Thai fruit flies were previously classified into 4 groups based on the quantitative differences in pericentric heterochromatin. Metaphase karyotypes of species Q, R, W, X, Y and Z are characterized by the presence of prominent blocks of pericentric heterochromatin in the X chromosomes and autosomes similar to the mitotic patterns found in B. kanchanaburi and B. raiensis. Hence, they are placed in Group 2 of this classification. Species U and V exhibit chromosome X patterns similar to that of B. carambolae and other related species. They are thus assigned to Group 4. In contrast, species S shows a minimum amount of pericentric heterochromatin in all autosomes, although the X chromosome follows the pattern of species Y. Interestingly, species T exhibits a unique pattern of euchromatin and heterochromatin in the X chromosome and conspicuous pericentric heterochromatin in all autosomes. Thus, species S and T are assigned to 2 new categories. Heterochromatin accumulations in the genome, as demonstrated in this study, appear to have played a significant role in chromosomal evolution. The different degree of variation in pericentric heterochromatin in mitotic chromosomes is, therefore, useful for cytotaxonomically distinguishing members of some cryptic species complexes of the dipteran insects.

Karyological studies of mediterranean stick-insects belonging to the generaClonopsisandLeptynia(Insecta Phasmatodea)

SUMMARYKaryotypes of three species of Clonopsis and of various populations of Leptynia hispanica and L. attenuata complexes were analyzed. The taxonomic status of the latter complexes is still uncertain. These genera include bisexual and parthenogenetic polyploid species and populations. The chromosomal numbers are: 2n = 32 in bisexual C. algerica, 2n = 22 in bisexual C. maroccana, 3n = 54 in telytokous C. gallica, 2n = 38 in bisexual Leptynia hispanica, 3n = 57 in telytokous triploid populations of L. hispanica, 4n = 76 in telytokous tetraploid populations of the same complex, 2n = 36 in a bisexual taxon of L. attenuata complex, 2n = 38 in an other bisexual taxon and 4n = 76 in a parthenogenetic tetraploid taxon of the same complex. All the karyotypes are described. It is postulated that pericentric inversions and centric fusions have played a relevant role in chromosomal evolution of these genera. Because hybridization is the more frequent mode of speciation in these stick-insects, the polyploidy, conne...

Karyotypes and meiosis of the Australian Tettigoniidae (Orthoptera) II. The genus Nanodectes Rentz (Tettigoniinae)*

The karyotypes and meioses from males of the species in the shield-backed katydid genus Nanodectes Rentz (Tettigoniinae) have been studied. The chromosome number of these species ranges from 2n = 15 to 2n =23 in the male. The male karyotypes were all X – 0 and the X was always the largest telocentric chromosome. Four types of chromosome systems are found in different populations of N. triodiae Rentz: 2n = 15 (6 metacentric + 8 telocentric autosomes + X), 2n = 15 (4 metacentric + 10 telocentric autosomes + X), 2n = 17 (4 metacentric+ 12 telocentric autosomes + X) and 2n = 19 (2 metacentric + 16 telocentric autosomes + X). Chromosome rearrangements, such as centric fusion and tandem fusion, appear to have played an important role in chromosome evolution at the inter- and intra-specific levels in Nanodectes. Possible pathways of karyotypic evolution and speciation are discussed.* Part I: pp. 303-51 in: 'The Tettigoniidae: Biology, Ecology, Systematics'. Eds W. J. Bailey and D. C. F. Rentz. (Crawford House: Bathurst.)

Chromosome systems in the North American Decticinae with reference to robertsonian changes (Orthoptera: Tettigoniidae).

Chromosome systems of 12 genera and 36 species of the North American Decticinae have been studied. The chromosome number of these species ranges from 2n=22 to 2n=31 in the male (see Table 2). Robertsonian changes has played an important role in chromosome evolution in these decticines. Neduba sp. has a neo-XY sex determining mechanism and Neduba diminutiva an X1X2Y one.The probable pathways of chromosome evolution and the origin of the neo-XY and -X1X2Y sex determining mechanisms are discussed, as well as the phylogeny and present taxonomic status of the North American Decticinae based on chromosome systems.

Detection of sister chromatid exchanges by 4'-6-diamidino-2-phenylindole fluorescence.

This paper describes a 4'-6-diamidino-2-phenylindole (DAPI) fluorescent technique for differentiation of sister chromatids and for the study of sister chromatid exchanges (SCE) in mouse chromosomes. The advantages of the DAPI fluorescent technique are also described. Differences in the occurrence of SCE between the centromeric heterochromatin (C-banded) and the chromosomal arm chromatin were studied in mouse cells (RAG) with or without mitomycin C treatment. Single strand exchanges between the DNA double helices in the sister chromatids were not detected. SCE and chromosome breakage appeared to occur more frequently in the centromeric region than in the chromosomal arm. This might play an important role in chromosome evolution in mice.