Chromosomal instability at common fragile sites in Seckel syndrome

Seckel syndrome (SCKL) is a rare, genetically heterogeneous disorder, with dysmorphic facial appearance, growth retardation, microcephaly, mental retardation, variable chromosomal instability, and hematological disorders. To date, three loci have been linked to this syndrome, and recently, the gene encoding ataxia-telangiectasia and Rad3-related protein (ATR) was identified as the gene mutated at the SCKL1 locus. The ATR mutation affects splicing efficiency, resulting in low levels of ATR in affected individuals. Elsewhere, we reported increased instability at common chromosomal fragile sites in cells lacking the replication checkpoint gene ATR. Here, we tested whether cells from patients carrying the SCKL1 mutation would show increased chromosome breakage following replication stress. We found that, compared with controls, there is greater chromosomal instability, particularly at fragile sites, in SCKL1-affected patient cells after treatment with aphidicolin, an inhibitor of DNA polymerase alpha and other polymerases. The difference in chromosomal instability between control and patient cells increases at higher levels of aphidicolin treatment, suggesting that the low level of ATR present in these patients is not sufficient to respond appropriately to replication stress. This is the first human genetic syndrome associated with increased chromosome instability at fragile sites following replication stress, and these findings may be related to the phenotypic findings in patients with SCKL1.     

Molecular parameters of genome instability: roles of fragile genes at common fragile sites

Common chromosome fragile sites occur at specific sequences within mammalian genomes that exhibit apparent single-stranded regions in mitotic chromosomes on exposure of cells to replication stress. Recent progress in the characterization of sequences, and more precise mapping of common fragile sites in mammalian and yeast genomes, has led to the exact placement of large common fragile regions straddling the borders of chromosomal G and R bands, with early and late replicating genomic regions, respectively, and could lead to breakthroughs in understanding the function of these evolutionarily conserved but highly recombinogenic chromosome elements. Deficiency of genes involved in DNA damage checkpoint responses, such as ATR, CHK1, HUS1 leads to increased frequency of fragile site instability. Some of these fragile sites, particularly FRA3B, encode genes that are themselves involved in the protection of cells from DNA damage through various mechanisms. Protection of mammalian genomes from accumulation of DNA damage in somatic cells is critical during development, puberty and during the reproductive lifespan, and occurs through mechanisms involving surveillance of the genome for damage, signals to the cell cycle machinery to stop cell cycle progression, signals to repair machinery to repair damage, signals to resume cycling or initiate apoptotic programs, depending on the extent of damage and repair. When genes involved in these processes are altered or deleted, cancer can occur. The tumor suppressor gene, FHIT at the FRA3B locus, and possibly other fragile genes, is a common target of damage and paradoxically encodes a protein with roles in protection from DNA damage.     

Aberrant breakpoints in chronic myelogenous leukaemia; oncogenes and fragile sites

Summary Three hundred and twenty-five aberrant breakpoints in chronic myelogenous leukaemia (CML) with Philadelphia chromosome variant were reviewed. Eight chromosomal bands (3p21, 6p21, 7p22, 11q13, 12p13, 17p13, 17q21, and 17q25) were found to be highly involved. Apart from 17q25, all these bands correspond to oncogenes sites and/or sites involved as primary breakpoints in cancer.This work was presented in part at the Congrès National d'Hématologie et de Transfusion Sanguine, March 1985 (Nouv Rev Fr Hématol, 1985, 27:72) and at the American Association for Cancer Research Meeting (Proceeding of the AACR 1986, 27:148)     

Genomic and epigenomic instability, fragile sites, schizophrenia and autism

Increasing evidence links genomic and epigenomic instability, including multiple fragile sites regions to neuropsychiatric diseases including schizophrenia and autism. Cancer is the only other disease associated with multiple fragile site regions, and genome and epigenomic instability is a characteristic of cancer. Research on cancer is far more advanced than research on neuropsychiatric disease; hence, insight into neuropsychiatric disease may be derived from cancer research results. Towards this end, this article will review the evidence linking schizophrenia and other neuropsychiatric diseases (especially autism) to genomic and epigenomic instability, and fragile sites. The results of studies on genetic, epigenetic and environmental components of schizophrenia and autism point to the importance of the folate-methionine-transulfuration metabolic hub that is diseases also perturbed in cancer. The idea that the folate-methionine-transulfuration hub is important in neuropsychiatric is exciting because this hub present novel targets for drug development, suggests some drugs used in cancer may be useful in neuropsychiatric disease, and raises the possibility that nutrition interventions may influence the severity, presentation, or dynamics of disease.     

Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species

Genus Pinus is a widely dispersed genus of conifer plants in the Northern Hemisphere. However, the inadequate accessibility of genomic knowledge limits our understanding of molecular phylogeny and evolution of Pinus species. In this study, the evolutionary features of complete plastid genome and the phylogeny of the Pinus genus were studied. A total of thirteen divergent hotspot regions (trnk-UUU, matK, trnQ-UUG, atpF, atpH, rpoC1, rpoC2, rpoB, ycf2, ycf1, trnD-GUC, trnY-GUA, and trnH-GUG) were identified that would be utilized as possible genetic markers for determination of phylogeny and population genetics analysis of Pinus species. Furthermore, seven genes (petD, psaI, psaM, matK, rps18, ycf1, and ycf2) with positive selection site in Pinus species were identified. Based on the whole genome this phylogenetic study showed that twenty-four Pinus species form a significant genealogical clade. Divergence time showed that the Pinus species originated about 100 million years ago (MYA) (95% HPD, 101.76.35–109.79 MYA), in lateral stages of Cretaceous. Moreover, two of the subgenera are consequently originated in 85.05 MYA (95% HPD, 81.04–88.02 MYA). This study provides a phylogenetic relationship and a chronological framework for the future study of the molecular evolution of the Pinus species.     

Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates

The concentration of evolutionary breakpoints in primate karyotypes in some particular regions or chromosome bands suggests that these chromosome regions are more prone to breakage. This is the first extensive comparative study which investigates a possible relationship of two genetic markers (intrachromosomal telomeric sequences [TTAGGG]n, [ITSs] and fragile sites [FSs]), which are implicated in the evolutionary process as well as in chromosome rearrangements. For this purpose, we have analyzed: (a) the cytogenetic expression of aphidicolin-induced FSs in Cebus apella and Cebus nigrivittatus (F. Cebidae, Platyrrhini) and Mandrillus sphinx (F. Cercopithecidae, Catarrhini), and (b) the intrachromosomal position of telomeric-like sequences by FISH with a synthetic (TTAGGG)n probe in C. apella chromosomes. The multinomial FSM statistical model allowed us to determinate 53 FSs in C. apella, 16 FSs in C. nigrivittatus and 50 FSs in M. sphinx. As expected, all telomeres hybridized with the probe, and 55 intrachromosomal loci were also detected in the Cebus apella karyotype. The chi(2) test indicates that the coincidence of the location of Cebus and Mandrillus FSs with the location of human FSs is significant (P < 0.005). Based on a comparative cytogenetic study among different primate species we have identified (or described) the chromosome bands in the karyotypes of Papionini and Cebus species implicated in evolutionary reorganizations. More than 80% of these evolutionary breakpoints are located in chromosome bands that express FSs and/or contain ITSs.     

Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications

Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.      

Good from far,but far from good: The impact of a reference genome on evolutionary inference

Genomic diversity and past population histories are key considerations in the fields of conservation and evolutionary biology. In this issue of Molecular Ecology Resources, Prasad et al. (Mol. Ecol. Resour., 2021) examine how the quality and phylogenetic divergence of reference genomes influences the outcomes of downstream analyses such as diversity and demographic history inference. Using the beluga whale and rowi kiwi as examples (Figure 1), they systematically estimate heterozygosity, runs of homozygosity (ROH), and demographic history (PSMC) using reference genomes of varying quality and phylogenetic divergence from the target species. They show that demographic history analyses are impacted by phylogenetic distance, although this is not pronounced until divergence exceeds 3% from the target species. Similarly, their results imply that heterozygosity estimates are dependent on phylogenetic distance and the method used to perform the estimates, and ROHs are potentially undetectable when a nonconspecific reference is used. This investigation into the role of divergence and quality of reference genomes highlights the impact and potential biases generated by genome selection on downstream analyses, and provides a possible alternative in cross-species scaffolding in instances where a conspecific reference genome is not available.     

Bovine genome mapping: evolutionary inference and the power of comparative genomics

All bovine chromosomes are now represented by a syntenic group, a linkage map and at least one in situ hybridization. Almost 1000 loci are mapped, about 300 of which are coding sequences useful for comparative mapping and evolutionary inference. Economically important loci are beginning to appear on bovine linkage maps and enhanced comparative maps are likely to be necessary to identify many of these genes by a comparative positional candidate gene approach.     

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.     

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference

SUMMARY: LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an alignment in a revealing way. LumberJack creates non-random jackknifed alignments by progressively sliding a window of omission along the alignment. A neighbor-joining tree is built from the full alignment and from each jackknifed alignment, and then the likelihood for each topology (given the original full alignment) is calculated. To determine whether any of the topologies generated is significantly more likely than the others, Kishino-Hasegawa, Shimodaira-Hasegawa and ELW tests are implemented. Availability and SUPPLEMENTARY INFORMATION: http://www.plantbio.uga.edu/~russell/software.html     

ITS sequence analysis and phylogenetic inference in the genus Lens mill

The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA from cultivated lentil (Lens culinaris subsp. culinaris) and its wild relatives was isolated and analysed for nucleotide sequence variation. Sequence divergence values ranged from no polymorphism within single species and between the cultigen and one accession of its wild progenitor (L. culinaris subsp. orientalis) to 14 base substitutions between L. nigricans and L. lamottei. Jukes and Cantor distance ranged from 0 to 1.79 %. Phylogenetic analysis confirmed the divergence of L. nigricans from all species, and the closeness of cultivated lentil to its wild progenitor, although two gene pools could possibly be identified in subsp. orientalis. Based on this study, the two recently recognized species, L. lamottei and L. tomentosus were separated from the other species. Each wild species showed peculiar autapomorphies and, in general, did not display much variation among accessions. The trees using chickpea as an outgroup formed two main clusters, one constituted by L. nigricans only and the other including the remaining taxa. Within this larger group, small subclades could be identified.     

Model dependence of the phylogenetic inference: relationship among carnivores, Perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences

Some previous analysis of mitochondrial proteins strongly support the Carnivora/Perissodactyla grouping excluding Cetartiodactyla (Artiodactyla + Cetacea) as an outgroup, but the support of the hypothesis remains equivocal from the analysis of several nuclear-encoded proteins. In order to evaluate the strength of the support by mitochondrial proteins, phylogenetic relationship among Carnivora, Perissodactyla, and Cetartiodactyla was estimated with the ML method by using the updated data set of the 12 mitochondrial proteins with several alternative models. The analyses demonstrate that the phylogenetic inference depends on the model used in the ML analysis; i.e., whether the site-heterogeneity is taken into account and whether the rate parameters are estimated for each individual proteins or for the concatenated sequences. Although the analysis of concatenated sequences strongly supports the Carnivora/Perissodactyla grouping, the total evaluation of the separate analyses of individual proteins, which approximates the data better than the concatenated analysis, gives only ambiguous results, and therefore it is concluded that more data are needed to resolve this trichotomy.     

On the correlation between composition and site-specific evolutionary rate: implications for phylogenetic inference

Model-based phylogenetic reconstruction methods traditionally assume homogeneity of nucleotide frequencies among sequence sites and lineages. Yet, heterogeneity in base composition is a characteristic shared by most biological sequences. Compositional variation in time, reflected in the compositional biases among contemporary sequences, has already been extensively studied, and its detrimental effects on phylogenetic estimates are known. However, fewer studies have focused on the effects of spatial compositional heterogeneity within genes. We show here that different sites in an alignment do not always share a unique compositional pattern, and we provide examples where nucleotide frequency trends are correlated with the site-specific rate of evolution in RNA genes. Spatial compositional heterogeneity is shown to affect the estimation of evolutionary parameters. With standard phylogenetic methods, estimates of equilibrium frequencies are found to be biased towards the composition observed at fast-evolving sites. Conversely, the ancestral composition estimates of some time-heterogeneous but spatially homogeneous methods are found to be biased towards frequencies observed at invariant and slow-evolving sites. The latter finding challenges the result of a previous study arguing against a hyperthermophilic last universal ancestor from the low apparent G + C content of its rRNA sequences. We propose a new model to account for compositional variation across sites. A Gaussian process prior is used to allow for a smooth change in composition with evolutionary rate. The model has been implemented in the phylogenetic inference software PHASE, and Bayesian methods can be used to obtain the model parameters. The results suggest that this model can accurately capture the observed trends in present-day RNA sequences.     

Chromosomal distributions of breakpoints in cancer,infertility, and evolution

We extract 11 genome-wide sets of breakpoint positions from databases on reciprocal translocations, inversions and deletions in neoplasms, reciprocal translocations and inversions in families carrying rearrangements and the human-mouse comparative map, and for each set of positions construct breakpoint distributions for the 44 autosomal arms. We identify and interpret four main types of distribution: (i) a uniform distribution associated both with families carrying translocations or inversions, and with the comparative map, (ii) telomerically skewed distributions of translocations or inversions detected consequent to births with malformations, (iii) medially clustered distributions of translocation and deletion breakpoints in tumor karyotypes, and (iv) bimodal translocation breakpoint distributions for chromosome arms containing telomeric proto-oncogenes.     

Chromosomal instability and aneuploidy in cancer: from yeast to man

Aneuploidy is frequently associated with disease and developmental abnormalities. It is also a key characteristic of cancer. Several model systems have been developed to study the role of chromosomal instability and aneuploidy in tumorigenesis. The results are surprisingly complex, with the conditions sometimes promoting and sometimes inhibiting tumour formation. Here, we review the effects of aneuploidy and chromosomal instability in cells and model systems of cancer, propose a model that could explain these complex findings and discuss how the aneuploid condition could be exploited in cancer therapy.     

The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions

Chelicerates are a diverse group of arthropods, with around 65,000 described species occupying a wide range of habitats. Many phylogenies describing the relationships between the various chelicerate orders have been proposed. While some relationships are widely accepted, others remain contentious. To increase the taxonomic sampling of species available for phylogenetic study based on mitochondrial genomes we produced the nearly complete sequence of the mitochondrial genome of the scorpion Mesobuthus gibbosus. Mitochondrial gene order in M. gibbosus largely mirrors that in Limulus polyphemus but tRNA secondary structures are truncated. A recent analysis argued that independent reversal of mitochondrial genome strand-bias in several groups of arthropods, including spiders and scorpions, could compromise phylogenetic reconstruction and proposed an evolutionary model that excludes mutational events caused by strand-bias (Neutral Transitions Excluded, NTE). An arthropod dataset of six mitochondrial genes, when analyzed under NTE, yields strong support for scorpions as sister taxon to the rest of Chelicerata. We investigated the robustness of this result by exploring the effect of adding additional chelicerate genes and taxa and comparing the phylogenies obtained under different models. We find evidence that (1) placement of scorpions arising at the base of the Chelicerata is an artifact of model mis-specification and scorpions are strongly supported as basal arachnids and (2) an expanded chelicerate dataset finds support for several proposed interordinal relationships (ticks plus mites [Acari] and spiders plus whip spiders plus whip scorpions [Araneae+Pedipalpi]). Mitochondrial sequence data are subject to systematic bias that is positively misleading for evolutionary inference and thus extreme methodological care must be taken when using them to infer phylogenies.     

The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects

The complete nucleotide sequences of the mt genome from the firefly, Pyrococelia rufa (Coeleoptera: Lampyridae) was determined. The circular genome is 17,739-bp long, and contains a typical gene complement, order, and arrangement identical to Drosophila yacuba. The presence of 1,724-bp long intergenic spacer in the P. rufa mt genome is unique. The putative initiation codon for ND1 gene appears to be TTG, instead of frequently found ATN. All tRNAs showed stable canonical clover-leaf structure of other mt tRNAs, except for tRNA(Ser) (AGN), DHU arm of which could not form stable stem-loop structure. Phylogenetic analysis among insect orders confirmed a monophyletic Endopterygota, a monophyletic Mecopterida, a monophyletic Diptera, a monophyletic Lepidoptera, and a monophyletic Coleoptera, suggesting that the complete insect mt genome sequence has a resolving power in the diversification events within Endopterygota. However, internal relationships among three coleopteran species are not clear, and the inclusion of some insect orders (i.e., apterygotan T. gertschi) in the analysis provided inconsistent results compared to other molecular studies.