A chromosome-based model for estimating the number of conserved segments between pairs of species from comparative genetic maps

Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.     

Evolutionary conserved chromosomal segments in the human karyotype are bounded by unstable chromosome bands

In this paper an ancestral karyotype for primates, defining for the first time the ancestral chromosome morphology and the banding patterns, is proposed, and the ancestral syntenic chromosomal segments are identified in the human karyotype. The chromosomal bands that are boundaries of ancestral segments are identified. We have analyzed from data published in the literature 35 different primate species from 19 genera, using the order Scandentia, as well as other published mammalian species as out-groups, and propose an ancestral chromosome number of 2n = 54 for primates, which includes the following chromosomal forms: 1(a+c(1)), 1(b+c(2)), 2a, 2b, 3/21, 4, 5, 6, 7a, 7b, 8, 9, 10a, 10b, 11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y. From this analysis, we have been able to point out the human chromosome bands more "prone" to breakage during the evolutionary pathways and/or pathology processes. We have observed that 89.09% of the human chromosome bands, which are boundaries for ancestral chromosome segments, contain common fragile sites and/or intrachromosomal telomeric-like sequences. A more in depth analysis of twelve different human chromosomes has allowed us to determine that 62.16% of the chromosomal bands implicated in inversions and 100% involved in fusions/fissions correspond to fragile sites, intrachromosomal telomeric-like sequences and/or bands significantly affected by X irradiation. In addition, 73% of the bands affected in pathological processes are co-localized in bands where fragile sites, intrachromosomal telomeric-like sequences, bands significantly affected by X irradiation and/or evolutionary chromosomal bands have been described. Our data also support the hypothesis that chromosomal breakages detected in pathological processes are not randomly distributed along the chromosomes, but rather concentrate in those important evolutionary chromosome bands which correspond to fragile sites and/or intrachromosomal telomeric-like sequences.     

Identifying functional links between genes using conserved chromosomal proximity

Conservation of proximity of a pair of genes across multiple genomes generally indicates that their functions could be linked. Here, we present a systematic evaluation using 42 complete microbial genomes from 25 phylogenetic groups to test the reliability of this observation in predicting function for genes. We find a relationship between the number of phylogenetic groups in which a gene pair is proximate and the probability that the pair belongs to a common pathway. Our method produces 1586 links between ortholog families substantiated by observed proximity in genomes representing at least three phylogenetic groups. Of the pairs annotated in the KEGG database, 80% are in the same biological pathway in KEGG.     

Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution

Mouse single chromosome paints were applied to rat prophase/prometaphase chromosomes to detect homologous chromosome regions. The analysis revealed 49 rat chromosomal regions ranging in size from whole chromosomes down to small bands near the limit of detection with this method, which was estimated to be 2-3 Mb. When all the painted regions were taken into account, the whole rat genome was covered with mouse-homologous regions, with the exception of small segments near the centromeres and the short arms of Chromosomes (Chrs) 3, 11, 12, and 13. These regions were shown to contain high levels of rat-specific repetitive DNA. The number of conserved segments between rat and mouse detected by our high-resolution zoo-FISH method was significantly higher than that reported in previous studies.     

Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D

Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic “types” than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (d_S). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments “universally conserved segments” (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics.     

Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis

DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis were identified, using the GenBank sequence database. Chromosomal locations of the conserved segments were compared between the two bacteria, and the following three features were observed. (1) Although the two genomes are nearly identical in size, chromosomal arrangements of the conserved segments are considerably different from each other. (2) In many cases, chromosomal locations of a conserved segment in the two species have deviated from each other by a multiple of 60°. (3) There are many instances in which a contiguous segment in one genome is split into two or more segments located at distinct positions in the other genome, and these split segments were found to tend to lie on the E. coli or B. subtilis genome separated by distances of multiples of 60°. On the basis of these observations, genome organizations of the two bacteria were discussed in terms of genome doublings as well as random chromosomal rearrangements.     

DNA sequence conservation at the gene level in a conserved chromosomal segment in twoPseudomonas species

A comparative analysis has been made of the DNA sequences of the isofunctional genes encodingN-acetylglutamate synthase of the arginine biosynthetic pathway of the bacterial speciesPseudomonas aeruginosa andPseudomonas putida. Overall homologies of 81% and 84% at the nucleotide and deduced amino acid sequence levels, respectively, were observed. This high homology was also reflected in the strikingly similar hydropathy profiles of the encoded proteins; patterns of codon usage, including rare codon usage; and amino acid composition of the proteins. This high level of homology at the DNA sequence level is consistent with the location of these genes in the genetically conserved chromosomal region (called auxotrophic-rich region) of the respectivePseudomonas species. Despite chromosomal rearrangements identified in this region the conservation observed at the chromosomal level between thesePseudomonas species is also maintained at the level of the DNA sequence, and in the deduced amino acid sequence, of the genes reported here and of six other pairs of genes of the tryptophan biosynthetic pathway, reported by others, which are also located within this chromosomal region.     

Extraordinarily conserved chromosomal synteny of Citrus species revealed by chromosome‐specific painting

Reliable identification of individual chromosomes in eukaryotic species is the foundation for comparative chromosome synteny and evolutionary studies. Unfortunately, chromosome identification has been a major challenge for plants with small chromosomes, such as the Citrus species. We developed oligonucleotide‐based chromosome painting probes for all nine chromosomes in Citrus maxima (Pummelo). We were able to identify all C. maxima chromosomes in the same metaphase cells using multiple rounds of sequential fluorescence in situ hybridization with the painting probes. We conducted comparative chromosome painting analysis in six different Citrus and related species. We found that each painting probe hybridized to only a single chromosome in all other five species, suggesting that the six species have maintained a complete chromosomal synteny after more than 9 million years of divergence. No interchromosomal rearrangement was identified in any species. These results support the hypothesis that karyotypes of woody species are more stable than herbaceous plants because woody plants need a longer period to fix chromosome structural variants in natural populations.     

Plant genome archaeology: evidence for conserved ancestral chromosome segments in dicotyledonous plant species

We have developed genetic maps, based on expressed sequence tags (ESTs) that are homologous to Arabidopsis genes, in four dicotyledonous crop plant species from different families. A comparison of these maps with the physical map of Arabidopsis reveals common genome segments that appear to have been conserved throughout the evolution of the dicots. In the four crop species analysed these segments comprise between 16 and 33% of the Arabidopsis genome. Our findings extend the synteny patterns previously observed only within plant families, and indicate that structural and functional information from the model species will be, at least in part, applicable in crop plants with large genomes.     

Highly conserved segments in mammalian chromosomes

Mammalian chromosomes from seven species for which gene maps exist were studied by high-resolution techniques to identify areas of conserved chromosome banding homology. High-resolution comparisons of human, chimpanzee, gorilla, orangutan, African green monkey, cat, and mouse chromosomes revealed regions of apparently conserved chromosomal banding, which may indicate the likely positions of conserved linkage in the phylogeny of mammals. This analysis indicates that many regions of subbanding homology may have remained intact during the evolution of mammals and reflects a high degree of chromosome conservation in diverse species.     

Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements

Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of <5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.     

Analysis of chromosomal homologies between two species of the subgenus sophophora: D. miranda and D. melanogaster using cloned DNA segments

Chromosomal homology between two species of the subgenus Sophophora, D. miranda and D. melanogaster, belonging to the obscura and the melanogaster group respectively, was probed by DNA in situ cross hybridizations. A set of recombinant plasmids with inserts derived from the D. melanogaster genome were cross hybridized to the D. miranda karyotype. Vice versa, recombinant Lambda phages isolated from a genomic D. miranda library were localized in D. miranda and probed for localization in D. melanogaster. In the main, the results support the homology relations proposed on the basis of cytogenetic data. However, the location of both tandemly repetitive genes tested, 5S RNA genes and the histone genes, is not in accordance with expectation. The 5S RNA genes, when probed with the D. melanogaster plasmid 12D8 (Artavanis-Tsakonas et al., 1977), were found to occur at two sites in both, D. miranda and D. pseudoobscura.     

Direct selection of DNA sequences conserved between species.

An essential requirement in the analysis of genomes is the identification of functionally important sequence elements, which are often evolutionarily conserved. We describe here the development of a novel procedure for the selective isolation of conserved sequences which is based on hybridization of PCR-amplifiable DNA fragments from the whole genome of one species to biotinylated DNA from a genomic region of another species. The interspecies DNA hybrids are immobilized and the PCR-amplifiable DNA fragments are eluted, amplified and after further hybridization-amplification rounds cloned. This method was used for the generation of sublibraries of conserved sequences from mouse and pig DNA from regions corresponding to cosmids from the human Xq28 region. Mouse and pig homologs of sequences containing exons of known human genes, as well as exons from novel genes have been identified.     

Homologous recombination between direct repeats of chromosomal segments comprising heterozygotic duplications in Escherichia coli

In conjugational matings between double mutants for the deo operon of Escherichia coli, haploid recombinants and extended tandem duplications deoC deoD/deoA deoB::Tn5 with the DeoC+DeoA+DeoB+DeoD- phenotype are formed (the deoD+ allele is not expressed due to the polar effect of the Tn5 insertion). Selection for the expression of the recessive deoC deoD alleles (in the thyA genome) leads to the segregation of haploid clones by duplications and also of clones that retain the diploidy but that are homozygous for deoC deoD. In addition to haploids, diploid clones retaining the duplications have also been found among the DeoD+ segregants. The phenotype of segregants retaining the duplication shows that they were formed by an unequal exchange between sister chromosomes. A comparison of segregation frequency of haploid and diploid DeoD+ clones in rec+ and recBC sbcB sbcC strains shows that duplications in the rec+ genome are more stable. On this basis, it is assumed that the RecBCD pathway possibly makes a greater contribution than the RecF pathway to the preservation of heterozygous duplications playing an important role in the evolution of prokaryotes.     

Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species

The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.     

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.     

Bayesian association-based fine mapping in small chromosomal segments

A Bayesian method for fine mapping is presented, which deals with multiallelic markers (with two or more alleles), unknown phase, missing data, multiple causal variants, and both continuous and binary phenotypes. We consider small chromosomal segments spanned by a dense set of closely linked markers and putative genes only at marker points. In the phenotypic model, locus-specific indicator variables are used to control inclusion in or exclusion from marker contributions. To account for covariance between consecutive loci and to control fluctuations in association signals along a candidate region we introduce a joint prior for the indicators that depends on genetic or physical map distances. The potential of the method, including posterior estimation of trait-associated loci, their effects, linkage disequilibrium pattern due to close linkage of loci, and the age of a causal variant (time to most recent common ancestor), is illustrated with the well-known cystic fibrosis and Friedreich ataxia data sets by assuming that haplotypes were not available. In addition, simulation analysis with large genetic distances is shown. Estimation of model parameters is based on Markov chain Monte Carlo (MCMC) sampling and is implemented using WinBUGS. The model specification code is freely available for research purposes from http://www.rni.helsinki.fi/~mjs/.