Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

Exceptional Chromosomal Evolution and Cryptic Speciation of Blind Mole Rats Nannospalax leucodon (Spalacinae, Rodentia) from South-Eastern Europe

Mole rats are exclusively subterranean and highly specialized rodents. Their long lifespans, remarkable anti-cancer mechanisms, and various distinctive adaptive features make them a useful research model. Moreover, opposing convergence of morphological traits, they have developed extremely high karyotype variability. Thus, 74 chromosomal forms have been described so far and new ones are being revealed continuously. These evolved during the process of rapid radiation and occur in different biogeographical regions. During research into their reproductive biology we have already provided substantial evidence for species-level separation of these taxa. Here, we review diverse chromosomal forms of the lesser blind mole rat, Mediterranean Nannospalax leucodon, distributed in South-eastern Europe, their karyotype records, biogeography, origin, and phylogeny from our extensive research. In the light of new data from molecular genetic studies, we question some former valuations and propose a cryptospecies rank for seven reproductively isolated chromosomal forms with sympatric and parapatric distribution and clear ecogeographical discrepances in their habitats, as well as new experimental and theoretical methods for understanding the courses of speciation of these unique fossorial mammals.

Cat Mammary Tumors: Genetic Models for the Human Counterpart

The records are not clear, but Man has been sheltering the cat inside his home for over 12,000 years. The close proximity of this companion animal, however, goes beyond sharing the same roof; it extends to the great similarity found at the cellular and molecular levels. Researchers have found a striking resemblance between subtypes of feline mammary tumors and their human counterparts that goes from the genes to the pathways involved in cancer initiation and progression. Spontaneous cat mammary pre-invasive intraepithelial lesions (hyperplasias and neoplasias) and malignant lesions seem to share a wide repertoire of molecular features with their human counterparts. In the present review, we tried to compile all the genetics aspects published (i.e., chromosomal alterations, critical cancer genes and their expression) regarding cat mammary tumors, which support the cat as a valuable alternative in vitro cell and animal model (i.e., cat mammary cell lines and the spontaneous tumors, respectively), but also to present a critical point of view of some of the issues that really need to be investigated in future research.

Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits

Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.

The pig X and Y Chromosomes: structure, sequence, and evolution

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Cytogenomics of Feline Cancers: Advances and Opportunities

Relative to the dog, integration of the cat into the “One Health” concept has been more restricted, particularly in the field of molecular oncology. Beyond the continual need to enhance the sophistication of feline healthcare per se, the unique spectrum of naturally-occurring cancers in the cat offers tremendous opportunities for comparative and translational advances that may have mutual benefit for human and veterinary medicine. The study of feline cancers additionally may generate new insight into underexplored aspects of tumor biology that are less accessible in other species, such as the relationship between chronic inflammation and neoplasia, and the role of viruses in malignant transformation. Several factors that have hindered molecular studies of feline cancers have now been surmounted, with the most fundamental step forward coming from the development of a high-quality reference genome sequence assembly for the cat. This article reviews landmark studies that have led to our current appreciation of feline genome architecture, and outlines techniques used in cancer cytogenomics, from conventional karyotyping analysis through to the development of genomic microarrays and beyond. A summary of progress in the identification and characterization of chromosomal aberrations in feline cancers is provided using examples from studies of injection-site sarcomas, lymphomas and mammary tumors.

Cloning and molecular characterization of telomerase reverse transcriptase (TERT) and telomere length analysis of Peromyscus leucopus

Telomerase reverse transcriptase (TERT) is the catalytic subunit of telomerase complex that regulates telomerase activity to maintain telomere length for all animals with linear chromosomes. As the Mus musculus (MM) laboratory mouse has very long telomeres compared to humans, a potential alternative animal model for telomere research is the Peromyscus leucopus (PL) mouse that has telomere lengths close to the human range and has the wild counterparts for comparison. We report the full TERT coding sequence (pTERT) from PL mice to use in the telomere research. Comparative analysis with eight other mammalian TERTs revealed a pTERT protein considerably homologous to other TERTs and preserved all TERT specific-sequence signatures, yet with some distinctive features. pTERT displayed the highest nucleotide and amino acid sequence homology with hamster TERT. Unlike human but similar to MM mice, pTERT expression was detected in various adult somatic tissues of PL mice, with the highest expression in testes. Four different captive stocks of PL mice and wild-captured PL mice each displayed group-specific average telomere lengths, with the longest and shortest telomeres in inbred and outbred stock mice, respectively. pTERT showed considerable numbers of synonymous and nonsynonymous mutations. A pTERT proximal promoter region cloned was homologous among PL and MM mice and rat, but with species-specific features. From PL mice, we further cloned and characterized ribosomal protein, large, P0 (pRPLP0) to use as an internal control for various assays. Peromyscus mice have been extensively used for various studies, including human diseases, for which pTERT and pRPLP0 would be useful tools.

A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans

The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents.

A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions

Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.

Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis

In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.

Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus

The order Rodentia and in particular the Muridae are characterised by extremely high rates of chromosome evolution and remarkable chromosome diversity. The Praomys group (Murinae, Muridae and Rodentia) constitutes a diverse and abundant group divided into two complexes, the jacksoni complex and the tullbergi complex which includes the species Praomys tullbergi. Comparative chromosome painting using the two index genomes, Mus musculus and Rattus norvegicus, was performed resulting in a high resolution chromosome map for P. tullbergi. The combined use of rat and mouse probes and the assistance of the assembly of all the available sequencing data from Ensembl genome browser allowed a great dissection of P. tullbergi genome, the detection of inversion events and ultimately the refinement of P. tullbergi comparative map. A key achievement was the reconstruction of a high precision Muroidea ancestral karyotype (Muridae/Cricetidae and Murine) based in a broad species analysis combining previous reported comparative maps together with the presented data. This permitted the reconstruction of the evolutionary history of chromosome changes since the ancestral Muroidea genome and enlightened the phylogenetic relationships with the related species mouse and rat. The analysis of constitutive heterochromatin and its co-localisation with the identified evolutionary breakpoints regions was performed suggesting the involvement of repetitive sequences in the chromosome rearrangements that originated the present P. tullbergi genome architecture.

Low, complex and probably reticulated chromosome evolution of Sciuromorpha (Rodentia) and Lagomorpha

Lagomorpha (rabbits and pikas) and Sciuromorpha (squirrels) are grouped in the Glires superorder. Their chromosome diversification, since their separation from the eutherian mammalian common ancestor, was characterized by a low rate of chromosome rearrangements. Consequently, the structure of some chromosomes was either conserved or only slightly modified, making their comparison easy at the genus, family and even order level. Interspecific in situ hybridization (Zoo-FISH) largely corroborates classical cytogenetic data but provides much more reliability in comparisons, especially for distant species. We reconstructed common ancestral karyotypes for Glires, Lagomorpha, Sciuromorpha, and Sciuridae species, and then, determined the chromosome changes separating these ancestors from their common eutherian ancestor. We propose that reticulated evolution occurred during the diversification of Glires, which implies that several pericentric inversions and Robertsonian translocations were conserved in the heterozygous status for an extensive period. Finally, among Lagomorpha and Sciuromorpha, we focused on Leporidae and Sciuridae chromosome evolution. In the various attempts to establish dichotomic evolutionary schemes, it was necessary to admit that multiple homoplasies (convergent and reverse rearrangements) occurred in Sciuridae and in a lesser degree, in Leporidae. In Leporidae, additional rearrangements were sufficient to propose a resolved phylogeny. However, a resolved phylogeny was not possible for Sciuridae because most of the rearrangements occurred in terminal branches. We conclude that a reticulated evolution took place early during the evolution of both families and lasted longer in Sciuridae than in Leporidae. In Sciuridae, most chromosome rearrangements were pericentric inversions involving short fragments. Such rearrangements have only mild meiotic consequences, which may explain the long persistence of the heterozygous status characterizing reticulated evolution.

Karyotypic evolution of hapalomys inferred from chromosome painting: a detailed characterization contributing new insights into the ancestral murinae karyotype

We report on the construction of a comparative chromosome map between the emblematic laboratory rat, Rattus norvegicus (RNO), and Delacour's Marmoset rat, Hapalomys delacouri (HDE), based on cross-species fluorescence in situ hybridization with R. norvegicus painting probes. Sixteen R. norvegicus chromosomes (RNO 3-6, 8, 10-15, 17-20, and X) were retained in their entirety (as a conserved block or as a single chromosome) in the H. delacouri genome. The remaining 5 R. norvegicus chromosomes (RNO 1, 2, 7, 9, and 16) produced 2 signals in the H. delacouri karyotype. Our analysis allowed the detection of an X-autosome translocation between RNO X and 11 that occurred convergently in an unrelated species, Bandicota savilei, and a single B chromosome that accounts for the 2n = 48 karyotype observed in this specimen. In total, the rat chromosome paints revealed 27 segments of conserved synteny in H. delacouri. The analysis showed 7 NOR bearing pairs in H. delacouri (HDE 1, 3, 6, 7, 8, 10, and 13) and the occurrence of an interstitial telomeric signal at the centromeric regions of 8 H. delacouri chromosomes (HDE 3, 10, 11, 12, 13, 16, 19, and 22). These data, together with published comparative maps, enabled a revision of the previously postulated murine ancestral condition suggesting that it probably comprised a wholly acrocentric karyotype with 2n = 46-50.

Chromosomal evolution in Rodentia

Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.

The genome diversity and karyotype evolution of mammals

The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.

Chromosomal evolution in Rattini (Muridae, Rodentia)

The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.

Chromosomal polymorphisms in African vlei rats, Otomys irroratus (Muridae: Otomyini), detected by banding techniques and chromosome painting: inversions, centromeric shifts and diploid number variation

Pericentric inversions are important for evolutionary biology because of their potential role in speciation. They may result in reproductive isolation due to illegitimate pairing of homologues at meiosis which leads to the production of aneuploid gametes (containing deletions or duplications of chromosomal segments), and consequently mediate chromosomal divergence. In this study, we describe the prevalence of pericentric inversions in the African vlei rat, Otomys irroratus (OIR). The species is characterized by intraspecific chromosomal variation (2n = 23-32) across its distribution in southern Africa. Here, we analyzed 55 individuals collected from 7 localities in South Africa by G- and C-banding and chromosome painting with flow sorts of Myotomys unisulcatus. Of the 55 specimens that were analyzed, 47% contained inversions or centromeric shifts on 4 autosomes (OIR1, 4, 6 and 10) which were present singly in specimens (i.e. none of the specimens contained all 4 inversions concurrently). These inversions were found in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggests that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes.

New insights into the karyotypic evolution in muroid rodents revealed by multicolor banding applying murine probes

Muroid rodents are composed of a wide range of species characterized by extensive karyotypic evolution. Even if this group includes such important laboratory animal models as domestic mouse (Mus musculus), Norway rat (Rattus norvegicus), Chinese hamster (Cricetulus griseus), and golden hamster (Mesocricetus auratus), comparative cytogenetic studies between rodents are difficult due to the characteristic rapid karyotypic evolution. Molecular cytogenetic methods can help resolve problems of comparing muroid chromosomes. Here, we used cross-species comparative multicolour banding with probes obtained from mouse chromosomes 3, 6, 18, and 19 to study the karyotypes of nine muroid species from the three subfamilies Murinae, Cricetinae, and Arvicolinae. Results from multicolour banding with these murine probes (mcb) allowed us to improve the comparative homology maps between these species and to obtain new insights into their karyotypic evolution. We identified evolutionary conserved chromosomal breakpoints and revealed four previously unrecognized homologous segments, four inversions, and 14 evolutionary new centromeres in the nine muroid species studied. We found Mus apomorphic rearrangements, not seen in other muroids, and defined several subfamily specific chromosome breaks, characteristic for Arvicolinae and Cricetinae. We show that mcb libraries are an effective tool both for the cytogenetic characterisation of important laboratory models such as the rat and hamster as well as elucidating the complex phylogenomics relationships of muroids.

Divergent patterns of breakpoint reuse in Muroid rodents

Multiple Genome Rearrangement (MGR) analysis was used to define the trajectory and pattern of chromosome rearrangement within muroid rodents. MGR was applied using 107 chromosome homologies between Mus, Rattus, Peromyscus, the muroid sister taxon Cricetulus griseus, and Sciurus carolinensis as a non-Muroidea outgroup, with specific attention paid to breakpoint reuse and centromere evolution. This analysis revealed a high level of chromosome breakpoint conservation between Rattus and Peromyscus and indicated that the chromosomes of Mus are highly derived. This analysis identified several conserved evolutionary breakpoints that have been reused multiple times during karyotypic evolution in rodents. Our data demonstrate a high level of reuse of breakpoints among muroid rodents, further supporting the "Fragile Breakage Model" of chromosome evolution. We provide the first analysis of rodent centromeres with respect to evolutionary breakpoints. By analyzing closely related rodent species we were able to clarify muroid rodent karyotypic evolution. We were also able to derive several high-resolution ancestral karyotypes and identify rearrangements specific to various stages of Muroidea evolution. These data were useful in further characterizing lineage-specific modes of chromosome evolution.

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Continuing advances in genomics are revealing substantial differences between genomes of major eukaryotic lineages. Because most data (in terms of depth and phylogenetic breadth) are available for angiosperms and mammals, we explore differences between these groups and show that angiosperms have less highly compartmentalized and more diverse genomes than mammals. In considering the causes of these differences, four mechanisms are highlighted: polyploidy, recombination, retrotransposition and genome silencing, which have different modes and time scales of activity. Angiosperm genomes are evolutionarily more dynamic and labile, whereas mammalian genomes are more stable at both the sequence and chromosome level. We suggest that fundamentally different life strategies and development feedback on the genome exist, influencing dynamics and evolutionary trajectories at all levels from the gene to the genome.

Chromosomal phylogeny of four Akodontini species (Rodentia, Cricetidae) from southern Brazil established by Zoo-FISH using Mus musculus (Muridae) painting probes

We established chromosome homology maps between Mus musculus (MMU) and five species of the Akodontini tribe, Akodon cursor (2n = 14, 15 and 16), A. montensis (2n = 24), A. paranaensis (2n = 44), A. serrensis (2n = 46) and Oligoryzomys flavescens (2n = 66) by Zoo-FISH (fluorescence in situ hybridization) using mouse chromosome-specific probes. The aims of this study were (1) to detect the chromosomal rearrangements responsible for the karyotype variation in this tribe and (2) to reconstruct the phylogenetic relationships among these species. We observed four common syntenic associations of homologous chromosome segments, of which the MMU 7/19 has been described previously in other rodents from Africa, Asia and Europe, and might represent a phylogenetic link between the Old World and Neotropical rodents. The remaining three associations (3/18, 6/12 and 8/13) have been observed exclusively in Neotropical rodents so far, which at present can be considered synapomorphic traits of this group. Five further mouse chromosomes (MMU 4, 9, 14, 18 and 19) were each found evolutionarily conserved as a separate syntenic unit. Our phylogenetic analysis using parsimony and heuristic search detected one consistent group, separating the Akodontini from other rodents.

Flying lemurs--the 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background

Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous.

Results

To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome.

Conclusion

Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

BACKGROUND

Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus.

RESULTS

Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome.

CONCLUSION

These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).

Chromosome homology between mouse and three Muridae species, Millardia meltada, Acomys dimidiatus and Micromys minutus, and conserved chromosome segments in murid karyotypes

Comparative chromosome painting with mouse (Mus musculus, MMU) chromosome-specific DNA probes was performed for three Muridae species, the Indian soft-furred field rat (Millardia meltada), the spiny mouse (Acomys dimidiatus) and the harvest mouse (Micromys minutus). All probes except for the Y probe were successfully hybridized to the chromosomes of all species, and homologous chromosome segments between mouse and the three species were identified at the molecular level. Comparison of our data with the published data of six other genera (Mus, Rattus, Apodemus, Otomys, Rhabdomys and Cricetulus) of the Muridae suggested that the associations MMU1b/17a, 2b/13a, 5b/11a, 7/19, 10b/17b, 10c/17c, 11b/16a, 12/17d and 13b/15, and the single painted chromosomes and chromosome segments MMU3, 4, 5a, 8a, 8b, 16b, 18 and X were probably contained by the ancestral karyotype of the Muridae, and have been strongly conserved throughout murid evolution.

Comparative chromosome painting map between two Ryukyu spiny rat species, Tokudaia osimensis and Tokudaia tokunoshimensis (Muridae, Rodentia)

Ryukyu spiny rats (genus Tokudaia) are indigenous species that are confined to three islands of the Nansei Shoto archipelago, Amami-Oshima, Tokunoshima and Okinawa-jima, Japan. Tokudaia tokunoshimensis from Tokunoshima Island and Tokudaia osimensis from Amami-Oshima Island are closely related taxonomically, although their karyotypes are quite different: the diploid chromosome numbers and sex chromosome constitution are 2n=45, X0/X0 for T. tokunoshimensis and 2n=25, X0/X0 for T. osimensis. We conducted comparative chromosome painting with chromosome-specific DNA probes of the laboratory mouse (Mus musculus) to molecularly examine the chromosome homology between T. tokunoshimensis and T. osimensis, and deduced a possible ancestral karyotype of Tokudaia species and the process of evolutionary chromosome rearrangements. The proposed ancestral karyotype with the diploid number of 2n=48, XX/XY was similar to the karyotype of T. tokunoshimensis, and the karyotype of T. osimensis would then have been established through at least 14 chromosomal changes, mainly centric fusion and tandem fusion, from the ancestral karyotype. The close karyological relationship between the ancestral karyotypes of Tokudaia and Apodemus also suggests that the chromosomal evolution in the Tokudaia-Apodemus lineage has been very slow and has accelerated only recently in the branch leading to T. osimensis.

Development of Y chromosome intraspecific polymorphic markers in the Felidae

Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.

Phylogenomics of the genus Mus (Rodentia; Muridae): extensive genome repatterning is not restricted to the house mouse

The house mouse (Mus musculus) is universally adopted as the mammalian laboratory model, and it is involved in most studies of large-scale comparative genomics. Paradoxically, this taxon is rarely the index species for evolutionary analyses of genome architecture owing to its highly rearranged karyotype. To unravel the origin and nature of this extensive repatterning genome, we performed a multidirectional chromosome painting study of representative species within the genus Mus. However, the latter includes four extant subgenera (Mus, Coelomys, Nannomys and Pyromys) between which the phylogenetic relationships remain elusive despite the numerous molecular studies. Comparative genomic maps were established using chromosome-specific painting probes of the laboratory mouse and Nannomys minutoides. Hence, by integrating closely related species within Mus, this study allowed us to: (i) unambiguously resolve for the first time the long-standing controversial phylogeny, (ii) trace the evolution of genome organization in the house mouse, (iii) track rearrangements that necessitated new centromere locations, i.e. formation of neocentromere or reactivation of latent centromeres, (iv) reveal an extremely high rate of karyotypic evolution, with a 10- to 30-fold acceleration which was coincidental with subgeneric cladogenesis and (v) highlight genomic areas of interest for high-resolution studies on neocentromere formation and synteny breakpoints.

Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). I. The genome homology of tundra vole, field vole, mouse and golden hamster revealed by comparative chromosome painting

Cross-species chromosome painting has become the mainstay of comparative cytogenetic and chromosome evolution studies. Here we have made a set of chromosomal painting probes for the field vole (Microtus agrestis) by DOP-PCR amplification of flow-sorted chromosomes. Together with painting probes of golden hamster (Mesocricetus auratus) and mouse (Mus musculus), the field vole probes have been hybridized onto the metaphases of the tundra vole (Microtus oeconomus). A comparative chromosome map between these two voles, golden hamster and mouse has been established based on the results of cross-species chromosome painting and G-banding comparisons. The sets of paints from the field vole, golden hamster and mouse identified a total of 27, 40 and 47 homologous autosomal regions, respectively, in the genome of tundra vole; 16, 41 and 51 fusion/fission rearrangements differentiate the karyotype of the tundra vole from the karyotypes of the field vole, golden hamster and mouse, respectively.

Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison

The evolutionary success of rodents of the superfamily Muroidea makes this taxon the most interesting for evolution studies, including study at the chromosomal level. Chromosome-specific painting probes from the Chinese hamster and the Syrian (golden) hamster were used to delimit homologous chromosomal segments among 15 hamster species from eight genera: Allocricetulus, Calomyscus, Cricetulus, Cricetus, Mesocricetus, Peromyscus, Phodopus and Tscherskia (Cricetidae, Muroidea, Rodentia). Based on results of chromosome painting and G-banding, comparative maps between 20 rodent species have been established. The integrated maps demonstrate a high level of karyotype conservation among species in the Cricetus group (Cricetus, Cricetulus, Allocricetulus) with Tscherskia as its sister group. Species within the genera Mesocricetus and Phodopus also show a high degree of chromosomal conservation. Our results substantiate many of the conclusions suggested by other data and strengthen the topology of the Muroidea phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. The derivation of the muroids karyotypes from the putative ancestral state involved centric fusions, fissions, addition of heterochromatic arms and a great number of inversions. Our results provide further insights into the karyotype relationships of all species investigated.

Chromosome painting in the manatee supports Afrotheria and Paenungulata

BACKGROUND

Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee.

RESULTS

The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19.

CONCLUSION

There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking afrotherian taxa.

Reciprocal chromosome painting between three laboratory rodent species

The laboratory mouse (Mus musculus, 2n = 40), the Chinese hamster (Cricetulus griseus, 2n = 22), and the golden (Syrian) hamster (Mesocricetus auratus, 2n = 44) are common laboratory animals, extensively used in biomedical research. In contrast with the mouse genome, which was sequenced and well characterized, the hamster species has been set aside. We constructed a chromosome paint set for the golden hamster, which for the first time allowed us to perform multidirectional chromosome painting between the golden hamster and the mouse and between the two species of hamster. From these data we constructed a detailed comparative chromosome map of the laboratory mouse and the two hamster species. The golden hamster painting probes revealed 25 autosomal segments in the Chinese hamster and 43 in the mouse. Using the Chinese hamster probes, 23 conserved segments were found in the golden hamster karyotype. The mouse probes revealed 42 conserved autosomal segments in the golden hamster karyotype. The two largest chromosomes of the Chinese hamster (1 and 2) are homologous to seven and five chromosomes of the golden hamster, respectively. The golden hamster karyotype can be transformed into the Chinese hamster karyotype by 15 fusions and 3 fissions. Previous reconstructions of the ancestral murid karyotype proposed diploid numbers from 2n = 52 to 2n = 54. By integrating the new multidirectional chromosome painting data presented here with previous comparative genomics data, we can propose that syntenies to mouse Chrs 6 and 16 were both present and to hypothesize a diploid number of 2n = 48 for the ancestral Murinae/Cricetinae karyotype.

Chromosome organization and chromatin modification: influence on genome function and evolution

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.

New members of the neurexin superfamily: multiple rodent homologues of the human CASPR5 gene

Proteins of the Caspr family are involved in cell contacts and communication in the nervous system. We identified and, by in silico reconstruction, compiled three orthologues of the human CASPR5 gene from the mouse genome, four from the rat genome, and one each from the chimpanzee, dog, opossum, and chicken genomes. Obviously, Caspr5 gene duplications have taken place during evolution of the rodent lineage. In the rat, the four paralogues are located in one chromosome arm, Chr 13p. In the mouse, however, the three Caspr5 genes are located in two chromosomes, Chr 1 and Chr 17. RT-PCR shows that all three mouse paralogues are being expressed. Common expression is found in brain tissue but different expression patterns are seen in other organs during fetal development and in the adult stage. Tissue specificity of expression has diverged during evolution of this young rodent gene family.

Cross-species chromosome painting

Comparative genomics is an important and expanding field of research, and the genome-wide comparison of the chromosome constitution of different species makes a major contribution to this field. Cross-species chromosome painting is a powerful technique for establishing chromosome homology maps, defining the sites of chromosome fusions and fissions, investigating chromosome rearrangements during evolution and constructing ancestral karyotypes. Here the protocol for cross-species chromosome painting is presented. It includes sections on cell culture and metaphase preparation, labeling of chromosome-specific DNA, fluorescent in situ hybridization (chromosome painting) and image analysis. Cell culture and metaphase preparation can take between 1 and 2 wk depending on the cell culture. Labeling of chromosome-specific DNA is completed in 1 d. Fluorescent in situ hybridization can be completed in a maximum of 4 d.

Genomic instability in rat: breakpoints induced by ionising radiation and interstitial telomeric-like sequences

The Norwegian rat (Rattus norvegicus) is the most widely studied experimental species in biomedical research although little is known about its chromosomal structure. The characterisation of possible unstable regions of the karyotype of this species would contribute to the better understanding of its genomic architecture. The cytogenetic effects of ionising radiation have been widely used for the study of genomic instability, and the importance of interstitial telomeric-like sequences (ITSs) in instability of the genome has also been reported in previous studies in vertebrates. In order to describe the unstable chromosomal regions of R. norvegicus, the distribution of breakpoints induced by X-irradiation and ITSs in its karyotype were analysed in this work. For the X-irradiation analysis, 52 foetuses (from 14 irradiated rats) were studied, 4803 metaphases were analysed, and a total of 456 breakpoints induced by X-rays were detected, located in 114 chromosomal bands, with 25 of them significantly affected by X-irradiation (hot spots). For the analysis of ITSs, three foetuses (from three rats) were studied, 305 metaphases were analysed and 121 ITSs were detected, widely distributed in the karyotype of this species. Seventy-six percent of all hot spots analysed in this study were co-localised with ITSs.

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.

Further insights into the ancestral murine karyotype: the contribution of the Otomys-Mus comparison using chromosome painting

The African vlei rat, Otomys irroratus, comprises several distinct chromosomal races that may be grouped into two major cytogenetic clades. Recognition of these clades is underpinned by a complex chromosomal rearrangement involving three different autosomes in the unfused state. We have used unidirectional fluorescence in situ hybridization (FISH) of mouse chromosome-specific painting probes to molecularly define the components of this rearrangement as well as to establish the chromosomal homologies between the mouse and the vlei rat genomes. This has allowed for the detection of 41 autosomal segments of conserved synteny. Nine mouse chromosomes were conserved in toto (MMU3, 4, 6, 7, 11, 12, 14, 18, 19) with a further seven (MMU2, 5, 8, 9, 10, 13, 16) showing homology to two discrete regions in the vlei rat genome. Two mouse autosomes (MMU15, 17) correspond to three regions in O. irroratus with MMU1 being the most fragmented showing five sites of hybridization in this species. By mapping these data to published sequence-based phylogenies we are able to confirm most of the published putative ancestral murine chromosomal states. Our data further indicate that MMU15a+ MMU13b+MMU10b+MMU17b was present in the murine ancestral karyotype suggesting an ancestral 2n = 52 rather than the 2n = 54 previously postulated.

Recent radiation in West African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes

West African gerbils of the genus Taterillus constitute a complex of seven sibling species distributed from sudano-guinean to saharo-sahelian regions. They display radically rearranged karyotypes despite low genic divergence and a very recent differentiation, that is, within the last 0.4 Myr for the six most derived species. We here provide a comparison of the seven specific karyotypes and perform a cladistic analysis using chromosomal rearrangements character states. When a posteriori polarized mutations were mapped onto the phylogenetic tree, 38 rearrangements were identified as fixed during the evolution of these rodents. This makes Taterillus one of the most striking examples of accelerated chromosomal evolution within placental mammals. Taking into account the types of chromosomal changes involved, divergence times between lineages, genetic distances, as well as reassessed geographic distributions, we suggest that (1) speciation in West African Taterillus was driven by chromosomal changes, and (2) the paleoclimatic oscillations of the Sahara desert have played a major role in their evolution. In particular, elevated plasticity of the Taterillus genome, as suggested by the patterns observed for some repetitive elements, would have led to a higher probability of mutation. We hypothesize that the process underpinning cladogenesis most probably involved highly underdominant genomic rearrangements that were fixed following pronounced populational bottlenecks resulting from drastic climatic and subsequent environmental changes. Major African rivers formed significant barriers to dispersal, limiting expansion during the more moist and so favorable periods. This scenario would explain the current parapatric species distributions and their relationship to the West African hydrographic features.

Molecular cytogenetics discards polyploidy in mammals

Polyploidy, the presence of more than two chromosome sets, is common in plants, but extremely rare in animals. The absence of polyploid organisms with well-differentiated sex chromosomes suggests that the disruption of the dosage between autosomes and sex chromosomes is incompatible with normal development. Thus, the announcement in 1999 of tetraploidy in a mammal, the South American red vizcacha rat Tympanoctomys barrerae, provoked great interest, even though the definitive proof of tetraploidy, the presence of four copies of each chromosome, was never provided. Here we used classical and molecular cytogenetics to test the ploidy level of T. barrerae and demonstrate that only two copies of each chromosome are present in this karyotype. The red vizcacha rat is clearly diploid and the amplification and dispersion of repetitive sequences best explain the large genome size of this mammal. Thus, polyploidy in mammals remains as unlikely as it has always been.

Alternate pathways of thyroid hormone metabolism

The major thyroid hormone (TH) secreted by the thyroid gland is thyroxine (T(4)). Triiodothyronine (T(3)), formed chiefly by deiodination of T(4), is the active hormone at the nuclear receptor, and it is generally accepted that deiodination is the major pathway regulating T(3) bioavailability in mammalian tissues. The alternate pathways, sulfation and glucuronidation of the phenolic hydroxyl group of iodothyronines, the oxidative deamination and decarboxylation of the alanine side chain to form iodothyroacetic acids, and ether link cleavage provide additional mechanisms for regulating the supply of active hormone. Sulfation may play a general role in regulation of iodothyronine metabolism, since sulfation of T(4) and T(3) markedly accelerates deiodination to the inactive metabolites, reverse triiodothyronine (rT(3)) and T(2). Sulfoconjugation is prominent during intrauterine development, particularly in the precocial species in the last trimester including humans and sheep, where it may serve both to regulate the supply of T(3), via sulfation followed by deiodination, and to facilitate maternal-fetal exchange of sulfated iodothyronines (e.g., 3,3'-diiodothyronine sulfate [T(2)S]). The resulting low serum T(3) may be important for normal fetal development in the late gestation. The possibility that T(2)S or its derivative, transferred from the fetus and appearing in maternal serum or urine, can serve as a marker of fetal thyroid function is being studied. Glucuronidation of TH often precedes biliary-fecal excretion of hormone. In rats, stimulation of glucuronidation by various drugs and toxins may lead to lower T(4) and T(3) levels, provocation of thyrotropin (TSH) secretion, and goiter. In man, drug induced stimulation of glucuronidation is limited to T(4), and does not usually compromise normal thyroid function. However, in hypothyroid subjects, higher doses of TH may be required to maintain euthyroidism when these drugs are given. In addition, glucuronidates and sulfated iodothyronines can be hydrolyzed to their precursors in gastrointestinal tract and various tissues. Thus, these conjugates can serve as a reservoir for biologically active iodothyronines (e.g., T(4), T(3), or T(2)). The acetic acid derivatives of T(4), tetrac and triac, are minor products in normal thyroid physiology. However, triac has a different pattern of receptor affinity than T(3), binding preferentially to the beta receptor. This makes it useful in the treatment of the syndrome of resistance to thyroid hormone action, where the typical mutation affects only the beta receptor. Thus, adequate binding to certain mutated beta receptors can be achieved without excessive stimulation of alpha receptors, which predominate in the heart. Ether link cleavage of TH is also a minor pathway in normal subjects. However, this pathway may become important during infections, when augmented TH breakdown by ether-link cleavage (ELC) may assist in bactericidal activity. There is a recent claim that decarboxylated derivates of thyronines, that is, monoiodothyronamine (T(1)am) and thyronamine (T(0)am), may be biologically important and have actions different from those of TH. Further information on these interesting derivatives is awaited.

Fluorescence in situ hybridization to chromosomes as a tool to understand human and primate genome evolution

For the last 15 years molecular cytogenetic techniques have been extensively used to study primate evolution. Molecular probes were helpful to distinguish mammalian chromosomes and chromosome segments on the basis of their DNA content rather than solely on morphological features such as banding patterns. Various landmark rearrangements have been identified for most of the nodes in primate phylogeny while chromosome banding still provides helpful reference maps. Fluorescence in situ hybridization (FISH) techniques were used with probes of different complexity including chromosome painting probes, probes derived from chromosome sub-regions and in the size of a single gene. Since more recently, in silico techniques have been applied to trace down evolutionarily derived chromosome rearrangements by searching the human and mouse genome sequence databases. More detailed breakpoint analyses of chromosome rearrangements that occurred during higher primate evolution also gave some insights into the molecular changes in chromosome rearrangements that occurred in evolution. Hardly any "fusion genes" as known from chromosome rearrangements in cancer cells or dramatic "position effects" of genes transferred to new sites in primate genomes have been reported yet. Most breakpoint regions have been identified within gene poor areas rich in repetitive elements and/or low copy repeats (segmental duplications). The progress in various molecular and molecular-cytogenetic approaches including the recently launched chimpanzee genome project suggests that these new tools will have a significant impact on the further understanding of human genome evolution.

Human, mouse, and rat genome large-scale rearrangements: stability versus speciation

Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation.