Biomedical subjects

Gauthier Dobigny

Publications and source records attributed to Gauthier Dobigny.

9 recordsLinked to original sources

PubMed2007

Evolutionary history of LINE-1 in the major clades of placental mammals.

BACKGROUND: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals. METHODOLOGY: To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed. PRINCIPAL FINDINGS: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis. SIGNIFICANCE: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

Animals↗

PubMed2006

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.

Animals↗

PubMed2006

Comparative genome maps of the pangolin, hedgehog, sloth, anteater and human revealed by cross-species chromosome painting: further insight into the ancestral karyotype and genome evolution of eutherian mammals.

To better understand the evolution of genome organization of eutherian mammals, comparative maps based on chromosome painting have been constructed between human and representative species of three eutherian orders: Xenarthra, Pholidota, and Eulipotyphla, as well as between representative species of the Carnivora and Pholidota. These maps demonstrate the conservation of such syntenic segment associations as HSA3/21, 4/8, 7/16, 12/22, 14/15 and 16/19 in Eulipotyphla, Pholidota and Xenarthra and thus further consolidate the notion that they form part of the ancestral karyotype of the eutherian mammals. Our study has revealed many potential ancestral syntenic associations of human chromosomal segments that serve to link the families as well as orders within the major superordinial eutherian clades defined by molecular markers. The HSA2/8 and 7/10 associations could be the cytogenetic signatures that unite the Xenarthrans, while the HSA1/19p could be a putative signature that links the Afrotheria and Xenarthra. But caution is required in the interpretation of apparently shared syntenic associations as detailed analyses also show examples of apparent convergent evolution that differ in breakpoints and extent of the involved segments.

Animals↗

PubMed2006

Absence of hypomethylation and LINE-1 amplification in a white x black rhinoceros hybrid.

Genomic stress resulting from the interspecific hybridization of marsupials has been shown to lead to hypomethylation and transposable element over-amplification. Here we investigated both methylation status and transposable element (LINE-1) activity in an F1 hybrid between the black (Diceros bicornis) and white rhinoceros (Ceratotherium simum). Our data show that in this instance the hybrid genome was not characterised by gross hypomethylation and LINE-1 over-amplification thus extending previous investigations on eutherian mammals. These findings underscore observations that wide-scale genomic instability involving hypomethylation and mobile element release may be marsupial specific phenomena within Mammalia.

Animals↗

PubMed2005

Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae).

Although they represent a quarter of the mammalian species, the evolutionary relationships among as well as within, the main murid lineages are still controversial. The subfamily Gerbillinae is no exception as previous studies based on morphological, karyotypical, and allozyme characters are highly incongruent. Here, we present the first molecular phylogeny for gerbils based on cytochrome b and 12S rRNA mitochondrial genes. Results are largely congruent between the two genes as well as with the concatenated data set with most of the nodes being well-supported. Based on the topologies retrieved here, we (1) propose the identification of three main clades, (2) support the split of Tatera genus into an Asian and an African group, the latter including Gerbillurus species, and (3) provide some evidence towards the inaccuracy of subgeneric divisions within both Gerbillus and Meriones. In addition, the sharp contrast between the genetic characters and morphological data sets suggest high levels of convergence, probably as a result of strong environmental constraints imposed on these rodents adapted to arid and semi-arid regions. Finally, molecular datings for the various cladogenetic events are in good agreement with the known gerbilline fossil record and support an African origin with subsequent migrations to Asia.

Africa↗

PubMed2004

LINE-1 distribution in Afrotheria and Xenarthra: implications for understanding the evolution of LINE-1 in eutherian genomes.

Long interspersed nuclear elements (LINEs) comprise about 21% of the human genome (of which L1 is most abundant) and are preferentially accumulated in AT-rich regions, as well as the X and Y chromosomes. Most knowledge of L1 distribution in mammals is restricted to human and mouse. Here we report the first investigation of L1 distribution in the genomes of a wide variety of eutherian mammals, including species in the two basal clades, Afrotheria and Xenarthra. Our results show L1 accumulation on the X of all eutherian mammals, an observation consistent with an ancestral involvement of these elements in the X-inactivation process (the Lyon repeat hypothesis). Surprisingly, conspicuous accumulation of L1 in AT-rich regions of the genome was not observed in any species outside of Euarchontoglires (represented by human, mouse and rabbit). Although several features were common to most species investigated, our comprehensive survey shows that the patterns observed in human and mouse are, in many aspects, far from typical for all mammals. We discuss these findings with reference to models that have previously been proposed to explain the AT distribution bias of L1 in human and mouse, and how this relates to the evolution of these elements in other eutherian genomes.

Animals↗

PubMed2004

LINE-1 amplification accompanies explosive genome repatterning in rodents.

Transposable elements (TEs) sometimes induce karyotypic changes following recombination, breakage and rearrangement. We used FISH and Southern blot analyses to investigate the amount and distribution of LINE-1 retrotransposons in rodents (genus Taterillus, Muridae, Gerbillinae) that have recently undergone an important genome repatterning. Our results were interpreted in a known phylogenetic framework and clearly showed that LINE-1 elements were greatly amplified and non-randomly distributed in the most rearranged karyotypes. A comparison between FISH and conventional banding patterns provided evidence that LINE-1 insertion sites and chromosome breakpoints were not strongly correlated, thus suggesting that LINE-1 amplification subsequently accompanied Taterillus chromosome evolution. Similar patterns are observed in some cases of genomic stresses (hybrid genomes, cancer and DNA-damaged cells) and usually associated with DNA hypomethylation. We propose that intensively repatterned genomes face transient stress phases during which some epigenetic features, such as DNA methylation, are relaxed, thus allowing TE amplification.

Animals↗

PubMed2004

Autosome and sex chromosome diversity among the African pygmy mice, subgenus Nannomys (Murinae; Mus).

The African pygmy mice, subgenus Nannomys, constitute the most speciose lineage of the genus Mus with 19 recognized species. Although morphologically very similar, they exhibit considerable chromosomal diversity which is here confirmed and extended by the G-banding analysis of 65 mice from West and South Africa. On the basis of their karyotype and distribution area, the specimens were assigned to at least five species. Extensive differentiation both within and between species was observed that involved almost exclusively Robertsonian translocations, 23 of which are newly described. Two of the rearrangements were sex chromosome-autosome translocations, associated in some cases with partial deletions of the X or Y chromosomes. Several authors have predicted that the highly deleterious effect of this rearrangement would be reduced if the sex and autosomal segments were insulated by a block of centromeric heterochromatin. The C-banding analyses performed showed that among the species carrying X-autosome translocations, one followed the expected pattern, while the other did not. In this case, functional isolation of the sex and autosome compartments must involve other repetitive sequences or genomic traits that require further molecular characterization. Such studies will provide insight into the causes and consequences of the high diversity of sex chromosome rearrangements in this subgenus.

Africa South of the Sahara↗

PubMed2004

Cytogenetics and cladistics.

Chromosomal data have been underutilized in phylogenetic investigations despite the obvious potential that cytogenetic studies have to reveal both structural and functional homologies among taxa. In large part this is associated with difficulties in scoring conventional and molecular cytogenetic information for phylogenetic analysis. The manner in which chromosomal data have been used by most authors in the past was often conceptionally flawed in terms of the methods and principles underpinning modern cladistics. We present herein a review of the different methods employed, examine their relative strengths, and then outline a simple approach that considers the chromosomal change as the character, and its presence or absence the character state. We test this using one simulated and several empirical data sets. Features that are unique to cytogenetic investigations, including B-chromosomes, heterochromatic additions/deletions, and the location and number of nucleolar organizer regions (NORs), as well as the weighting of chromosomal characters, are critically discussed with regard to their suitability for phylogenetic reconstruction. We conclude that each of these classes of data have inherent problems that limit their usefulness in phylogenetic analyses and in most of these instances, inclusion should be subject to rigorous appraisal that addresses the criterion of unequivocal homology.

Chromosomes↗