Mitochondrial DNA and karyotypic data confirm the presence of Mus indutus and Mus minutoides (Mammalia, Rodentia, Muridae, Nannomys) in Botswana.
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ABSTRACT:
SUBMITTER: McDonough MM
PROVIDER: S-EPMC3867174 | biostudies-literature | 2013
REPOSITORIES: biostudies-literature
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Project description:BackgroundRecent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus Mus which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres.ResultsThe chromosomal distribution of rDNA clusters was determined by in situ hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood analyses. Our results highlighted the following features of rDNA cluster dynamics in the genus Mus: i) rDNA clusters showed extensive diversity in number between species and an almost exclusive pericentromeric location, ii) a strong association between rDNA sites and centromeres was retrieved which may be related to their shared constraint of concerted evolution, iii) 24% of the observed breakpoints mapped near an rDNA cluster, and iv) a substantial rate of rDNA cluster change (insertion, deletion) also occurred in the absence of chromosomal rearrangements.ConclusionsThis study on the dynamics of rDNA clusters within the genus Mus has revealed a strong evolutionary relationship between rDNA clusters and centromeres. Both of these genomic structures coincide with breakpoints in the genus Mus, suggesting that the accumulation of a large number of repeats in the centromeric region may contribute to the high level of chromosome repatterning observed in this group. However, the elevated rate of rDNA change observed in the chromosomally invariant clade indicates that the presence of these sequences is insufficient to lead to genome instability. In agreement with recent studies, these results suggest that additional factors such as modifications of the epigenetic state of DNA may be required to trigger evolutionary plasticity.
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Project description:Niviventer sacer (Rodentia: Muridae) had been regarded as a subspecies of N. confucianus, i.e. N. c. sacer, and was raised as a distinct species recently by our laboratory. We sequenced the complete mitochondrial genome of N. sacer first and annotated the genome structure. The total length of the genome was 16,308 base pairs (bp) containing 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. We also constructed the phylogenetic tree by maximum-likelihood method and it demonstrated that N. sacer was the sister clade of N. confucianus.
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Project description:Recent surveys of the human genome have highlighted the significance of balancing selection in relation to understanding the evolutionary origins of disease-associated variation. Cis-regulatory variation at the blood group-related glycosyltransferase B4galnt2 is associated with a phenotype in mice that closely resembles a common human bleeding disorder, von Willebrand disease. In this study, we have performed a survey of the 5' flanking region of the B4galnt2 gene in several Mus musculus subspecies and Mus spretus. Our results reveal a clear pattern of trans-species polymorphism and indicate that allele classes conferring alternative tissue-specific expression patterns have been maintained for >2.8 My in the genus Mus. Furthermore, analysis of B4galnt2 expression patterns revealed the presence of an additional functional class of alleles, supporting a role for gastrointestinal phenotypes in the long-term maintenance of expression variation at this gene.
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Project description: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.
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Project description:Aspiculuris tetraptera a pinworm of mice, is an important parasite in institutions with mice colonies for both research and teaching purposes. Infection with this parasite has impact on biomedical research. This is likely due to the availability of the parasite's eggs in the environment, therefore can easily be transmitted and infection is generally asymptomatic. No information regarding the prevalence, morphology or phylogeny is available on A. tetraptera from Saudi Arabia. A group of 50 laboratory mice were investigated for the presence of A. tetraptera. Worms were described morphologically and molecular characterization was attempted using 18S rRNA and Cytochrome Oxidase Subunit I genes. The prevalence of A. tetraptera infestation in the laboratory mice examined was found to be 46%. Morphological description indicated that the worms belong to A. tetraptera and this was confirmed by molecular characterization. Both regions studied have shown that the worm under investigation grouped with A. tetraptera. 18S rDNA sequences obtained in the present study showed high identity with sequences from A. tetraptera while Cytochrome c Oxidase subunit I gene (COI) sequences showed intraspecific variation resulted into two haplotypes from the isolates in the present study. A. tetraptera was recorded for the first time from Saudi Arabia. Molecular characterization has shown, based on the COI sequences, that the Saudi isolates of A. tetraptera are distinct.
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Project description:The marmoset rats (Hapalomys delacouri) is a rarely investigated rodent. It occupies important ecological niche and phylogenetic position. The complete mitochondrial genome of H. delacouri was determined for the first time by long PCR and second-generation sequencing. The results showed that the entire mitogenome of H. delacouri was 16,316 bp long (deposited in GenBank with accession number MK850463). The gene order and orientation were the same as the most rodent. Only tRNALys (TTT) and tRNASer (AGN) of 22 transfer RNAs showed atypical cloverleaf structures, lacking a dihydrouridine (DHU) arm. The newly added H. delacouri mitogenome will benefit population genetic and phylogenetic studies in the rodent.
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Project description:The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.
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Project description:The complete mitochondrial genome of the Tamarisk jird, Meriones tamariscinus, was sequenced. The 16,389bp genome contains 37 genes, typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.8%, with a base composition of 34.0% A, 24.5% C, 12.3% G, and 29.2% T. The phylogenetic analysis showed that M. tamariscinus was classified in the genus Meriones, Muridae.
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Project description:The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.
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