New karyotypic data for Asian rodents (Rodentia, Muridae) with the first report of B-chromosomes in the genusMus

Retrospective Survey of Borrelia spp. From Rodents and Ticks in Thailand

Borrelia is a genus of spirochetal bacteria with several species known to cause disease in humans. The distribution of Borrelia has rarely been studied in Thailand. In this study, a retrospective survey of Borrelia was conducted in ticks and wild rodents to better characterize the prevalence, diversity, and distribution of Borrelia across Thailand. Several pools of DNA from tick samples were positive for Borrelia spp. (36/258, 13.9%). Borrelia theileri/B. lonestari was found in 17 tick samples (16 pools of Haemaphysalis bandicota and 1 pool of Rhipicephalus sp.), and Borrelia yangtzensis was found in 8 tick samples (2 pools of H. bandicota and 6 pools of Ixodes granulatus). Borrelia spp. were detected at low prevalence levels in rodent tissue samples (24/2001, 1.2%), with 19 identified as B. theileri or B. lonestari and 5 identified as B. miyamotoi. Several geographic and species-specific infection trends were apparent, with Ixodes ticks infected with B. yangtzensis and Haemaphysalis and Rhipicephalus ticks infected with both B. yangtzensis and B. theileri/B. lonestari. Notably, B. yangtzensis showed a similar geographic distribution to B. miyamotoi, which was identified in new areas of Thailand in this study. The flagellin gene sequence from B. miyamotoi was more similar to European (99.3-99.9%) than Japanese (96.9-97.6%) genotypes. This study greatly expands the knowledge of Borrelia in Thailand and identified several Borrelia species for the first time. It also found several ticks and rodents infected with the pathogen that were not previously known to carry Borrelia.

Chromosomal polymorphism in mammals: an evolutionary perspective

Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

This review aims to synthesise knowledge regarding the taxonomy of South-east Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specialisations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analysed the prevalence of major rodent-borne diseases in South-east Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rain-fed and irrigated landscapes, generally in and around rice fields.

Non-Sciuromorph rodent karyotypes in evolution

Rodents are, taxonomically, the most species-rich mammalian order. They display a series of special genomic features including the highest karyotypic diversity, frequent occurrence of complex intraspecies chromosome variability, and a variety of unusual chromosomal sex determination mechanisms not encountered in other mammalian taxa. Rodents also have an abundance of cytochemically heterogeneous heterochromatin. There are also instances of extremely rapid karyotype reorganization and speciation not accompanied by significant genetic differentiation. All these peculiarities make it clear that a detailed study of rodent genomic evolution is indispensable to understand the mode and tempo of mammalian evolution. The aim of this review is to update the data obtained by classical and molecular cytogenetics as well as comparative genomics in order to outline the range of old and emerging problems that remain to be resolved.

Host cell/Orientia tsutsugamushi interactions: evolution and expression of syndecan-4 in Asian rodents (Rodentia, Muridae)

Scrub typhus is an acute febrile zoonotic disease and worldwide more than a billion people may be at risk for infection. Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium. Rodents are reported to be the primary reservoir hosts of the disease and according to the most recent surveys, all species within the Rattus sensu lato complex of the tribe Rattini are carriers of scrub typhus. There is no evidence that any of mouse (Mus) species serves as the primary reservoir of the bacterium even when occurring in sympatry with wild infected rats. This contrast in the host/syndecan-4 interactions between Rattini and Asian Murini may be due to intrinsic (i.e., genetic) differences. Herein we compare the sequence and expression levels of syndecan-4 (the putative cell receptor of O. tsutsugamushi) between Rattini species that are known to be natural reservoirs for the typhus agents, and Murini species that are not. Although it was not possible to conclusively link the structural variations detected in syndecan-4 with carrier status in either Rattini and Murini, our findings indicate the absence of a strong Orientia-mediated selective regime acting on gene structure. In contrast, variable spleen-specific syndecan-4 expression levels show a strong correlation between under-expression of syndecan-4 in Murini and seropositive Rattini, compared to seronegative Rattini rodents. We postulate that two divergent responses may be at work in Murini and Rattini, both linked with differential expression of syndecan-4: (i) reduced syndecan-4 transcription in Murini decreases the likelihood that the host cells will become infected by the Orientia bacterium, while (ii) reduced syndecan-4 expression in seropositive Rattini limits the pathogenicity of Orientia and consequently improves the longevity of the rat hosts. These patterns may underpin the poor carrier status of wild mice on the one hand, and the effective role of wild rats as reservoir hosts on the other.

Molecular demonstration of Trypanosoma evansi and Trypanosoma lewisi DNA in wild rodents from Cambodia, Lao PDR and Thailand

In this study, we investigated the molecular evidence of Trypanosoma evansi in wild rodents from Cambodia, Lao PDR and Thailand. Between November 2007 and June 2009, 1664 rodents were trapped at eight sites representative of various ecological habitats. Of those animals, 94 were tested by direct microscopic blood examination, 633 using the Card Agglutination Test for Trypanosomes (CATT/T. evansi) and 145 by Polymerase Chain Reaction (PCR) with two sets of primers: TRYP1 (amplifying ITS1 of ribosomal DNA of all trypanosomes) and TBR (amplifying satellite genomic DNA of Trypanozoon parasites). Using TRYP1, based on the size of the PCR products, 15 samples from the three countries were positive for Trypanosoma lewisi (two were confirmed by sequencing), and three were positive for Trypanozoon (one was confirmed by sequencing and three by TBR primers); the specificity of the primers failed as rodent DNA was amplified in some cases. Using TBR, six samples were positive for Trypanozoon (one was confirmed by sequencing); as T. evansi is the only species of the Trypanozoon sub-genus possibly present in Asian rodents, these results confirmed its presence in rodents from Thailand (Rattus tanezumi) and Cambodia (R. tanezumi, Niviventer fulvescens & Maxomys surifer). Further investigations are necessary to establish the situation in Lao PDR. None of the 16 samples most strongly positive to the CATT proved to be positive for Trypanozoon by PCR. The merits of the CATT for such studies were not confirmed. Studying the urban and rural circulation of these parasites in rodents will enable an evaluation of human exposure and infection risk, as human infections by T. evansi were recently described in India and by T. lewisi in India and Thailand. As sequencing PCR products is expensive, the development of new molecular and serological tools for rodents would be very useful.

Karyotypes of two rare rodents, Hapalomys delacouri and Typhlomys cinereus (Mammalia, Rodentia), from Vietnam

Karyotypes of Hapalomys delacouri (Rodentia, Muridae) and Typhlomys cinereus (Rodentia, Platacanthomyidae) from Vietnam are described for the first time. The diploid karyotype of Hapalomys delacouri is 38 (NFa=48), consisting of six pairs of bi-armed and 12 pairs of acrocentric autosomes decreasing in size; plus a large metacentric X chromosome and Y chromosome, also metacentric, that is equal in size to the largest pair of acrocentric autosomes. The newly described karyotype differs significantly from that reported for Hapalomys delacouri from northern Thailand. The latter record very likely represents a different species of Hapalomys, possibly the taxon Hapalomys pasquieri described from north-central Laos.The diploid karyotype of Typhlomys cinereus is 38 (NF=48), consisting of five pairs of meta- to submetacentric and 14 pairs of acrocentric chromosomes varying in size from large to small; sex chromosomes were not defined.

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.

Multiple geographic origins of commensalism and complex dispersal history of Black Rats

The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

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.