Chromosomal characterization of Arvicanthis species (Rodentia, Murinae) from western and central Africa: implications for taxonomy

Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human

The African grass or Nile rat (NR) (Arvicanthis niloticus) is a herbivorous diurnal rodent which is used as a biological model for research on type 2 diabetes mellitus (T2DM) and the circadian rhythm. Similar to humans, male NRs develop T2DM with high-carbohydrate diets. The NR thus provides a unique opportunity to identify the nutritional and underlying genetic factors that characterise human T2DM, as well as the effects of potential anti-diabetic phytochemicals such as Water-Soluble Palm Fruit Extract. Whole genome sequencing (WGS) could help identify possible genetic causes why NRs spontaneously develop T2DM in captivity. In this study, we performed WGS on a hepatic deoxyribonucleic acid (DNA) sample isolated from a male NR using PacBio high-fidelity long-read sequencing. The WGS data obtained were then de novo assembled and annotated using PacBio HiFi isoform sequencing (Iso-Seq) data as well as previous Illumina RNA sequencing (RNA-Seq) data. Genes related to insulin and circadian rhythm pathways were present in the NR genome, similar to orthologues in the rat, mouse and human genomes. T2DM development in the NR is thus most likely not attributable to structural differences in these genes when compared to other biological models. Further studies are warranted to gain additional insights on the genetic-environmental factors which underlie the genetic permissiveness of NRs to develop T2DM.

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Background

The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.

Results

We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.

Conclusions

Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Time-shifting effects of methylphenidate on daily rhythms in the diurnal rodent Arvicanthis ansorgei

People suffering of attention-deficit/hyperactivity disorder (ADHD) and treated with the psychostimulant methylphenidate (MPH) show sleep-wake cycle and daily rhythm alterations despite the beneficial effects of MPH on behavioral symptoms (i.e., hyperactivity, attention). In nocturnal rodents (i.e., mice), chronic exposure to MPH alters the neural activity of the circadian clock in the suprachiasmatic nucleus (SCN), behavioral rhythms, and the sleep-wake cycle. Here, we studied the effects of MPH on daily rhythms of behavior and body temperature of the diurnal rodent Arvicanthis ansorgei. Under a light-dark cycle, chronic exposure to MPH in drinking water delayed the onset of both activity and body temperature rhythms. Interestingly, delays were larger when MPH access was restricted to the first 6 h of the light phase (i.e., activity phase) of the 24-h cycle. Since MPH effects are dependent on animal's fluid intake, in a last experiment, we controlled the time and dose of MPH delivery in Arvicanthis using an intraperitoneal perfusion method. Similarly to the experiment with MPH in drinking water, Arvicanthis showed a delay in the onset of general activity and body temperature when MPH infusions, but not vehicle, were during the first 6 h of the light phase. This study indicates that MPH alters daily rhythms in a time-dependent manner and proposes the use of a diurnal rodent for the study of the effects of MPH on the circadian clock. Knowing the circadian modulation on the effects of MPH in behavior could give new insights in the treatment of ADHD.

Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats

Background

The Nile rat (NR, Arvicanthis niloticus) is a model of carbohydrate-induced type 2 diabetes mellitus (T2DM) and the metabolic syndrome. A previous study found that palm fruit juice (PFJ) delayed or prevented diabetes and in some cases even reversed its early stages in young NRs. However, the molecular mechanisms by which PFJ exerts these anti-diabetic effects are unknown. In this study, the transcriptomic effects of PFJ were studied in young male NRs, using microarray gene expression analysis.

Methods

Three-week-old weanling NRs were fed either a high-carbohydrate diet (%En from carbohydrate/fat/protein = 70:10:20, 16.7 kJ/g; n = 8) or the same high-carbohydrate diet supplemented with PFJ (415 ml of 13,000-ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal; n = 8). Livers were obtained from these NRs for microarray gene expression analysis using Illumina MouseRef-8 Version 2 Expression BeadChips. Microarray data were analysed along with the physiological parameters of diabetes.

Results

Compared to the control group, 71 genes were up-regulated while 108 were down-regulated in the group supplemented with PFJ. Among hepatic genes up-regulated were apolipoproteins related to high-density lipoproteins (HDL) and genes involved in hepatic detoxification, while those down-regulated were related to insulin signalling and fibrosis.

Conclusion

The results obtained suggest that the anti-diabetic effects of PFJ may be due to mechanisms other than an increase in insulin secretion.

Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history

A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.

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.

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.

Retinal anatomy and visual performance in a diurnal cone-rich laboratory rodent, the Nile grass rat (Arvicanthis niloticus)

Unlike laboratory rats and mice, muridae of the Arvicanthis family (A. ansorgei and A. niloticus) are adapted to functioning best in daylight. To date, they have been used as experimental models mainly in studies of circadian rhythms. However, recent work aimed at optimizing photoreceptor-directed gene delivery vectors (Khani et al. [2007] Invest Ophthalmol Vis Sci 48:3954-3961) suggests their potential usefulness for studying retinal pathologies and therapies. In the present study we analyzed the retinal anatomy and visual performance of the Nile grass rat (A. niloticus) using immunohistofluorescence and the optokinetic response (OKR). We found that approximately 35-40% of photoreceptors are cones; that many neural features of the inner retina are similar to those in other diurnal mammals; and that spatial acuity, measured by the OKR, is more than two times that of the usual laboratory rodents. These observations are consistent with the known diurnal habits of this animal, and further support its pertinence as a complementary model for studies of structure, function, and pathology in cone-rich mammalian retinae.

Systematics and phylogeny of West African gerbils of the genus Gerbilliscus (Muridae: Gerbillinae) inferred from comparative G- and C-banding chromosomal analyses

Comparative analysis of the G- and C-banding patterns in six morphologically similar species of the genus Gerbilliscus(G. gambianus, G. guineae, G. kempi, Gerbilliscus sp., G. robustus and G. leucogaster) and one belonging to the genus Gerbillurus (G. tytonis) from 27 West, East and South African localities was carried out. Our study revealed that 17 rearrangements comprising seven fissions, five translocations and five inversions occurred in the evolution of this group, with 1-13 rearrangements differentiating the various species. In addition the unusually large sex chromosomes appear to be species-specific as judged by size and morphology reflecting structural rearrangements as well as the variable presence of a large amount of C-heterochromatin found in each species at a particular chromosomal location. These karyotypic features allow us to recognize five distinct species in West Africa (compared to the two recognized in recent taxonomic lists) and to roughly delimit their geographical distributions. The pattern of phylogenetic relationships inferred from a cladistic analysis of the chromosomal data is in good agreement with recent molecular phylogenetic studies that recognize a West African species group within the genus Gerbilliscus, and the monophyly of both Gerbilliscus and Gerbillurus.

Polymorphic karyotypes and sex chromosomes in the tufted deer (Elaphodus cephalophus): cytogenetic studies and analyses of sex chromosome-linked genes

Different diploid chromosome numbers have been reported for the tufted deer Elaphodus cephalophus (female, 2n = 46/47; male, 2n = 47/48) in earlier reports. In the present study, chromosomal analysis of seven tufted deer (5 male symbol, 2 female symbol) revealed that the karyotype of these animals contains 48 chromosomes, including a pair of large heteromorphic chromosomes in the male. C-banding revealed these chromosomes to be very rich in constitutive heterochromatin. Chromosome banding and PCR of sex chromosome-linked genes (SRY, ZFX, ZFY) performed on DOP-PCR products of single microdissected X and Y chromosomes confirmed that the large telocentric chromosome without secondary constriction is the X chromosome whereas the subtelocentric chromosome is the Y. The increased size of both, the X and Y chromosome, appears to be at least partially attributable to the presence of substantial amounts of heterochromatin.

Mitochondrial phylogeny reveals differential modes of chromosomal evolution in the genus Tatera (Rodentia: Gerbillinae) in Africa

The African gerbils of the genus Tatera are widespread and abundant throughout sub-Saharan Africa. There is still today a certain controversy concerning the taxonomy of these rodents and very few attempts have been made to assess their systematic relationships. The present paper introduces findings based on the partial sequences of cytochrome b (495 bp) and the 16S rRNA (469 bp) mitochondrial genes of six (T. robusta, T. nigricauda, T. vicina, T. leucogaster, T. valida, and T. kempi) species together with two additional taxa. We also report the karyotypes of T. vicina and T. leucogaster. We propose that T. vicina should be considered as a valid species and show the monophyly of the robusta species group, with the exclusion of T. leucogaster. Our results show there is a different chromosomal evolutionary pattern within the two major lineages, which is recognizable through molecular phylogenetics. One is characterized by karyotype stability and the other by a considerable number of chromosomal rearrangements. The lineage divergence coincides with the formation of the East African Rift. The processes that led to the origin of the East African species seem to be related to the subsequent climatic changes, which caused cyclic contraction and expansion of the savannah biomes. Furthermore, geological activities that characterized East Africa during Plio-Pleistocene may also have contributed to lineage divergence.

The Nile grass rat as a laboratory animal

Rodents are the subjects of the overwhelming majority of laboratory animal studies, and most laboratory rodents are nocturnal. The availability of a suitable diurnal rodent would provide a more effective animal model for biomedical research applicable to humans. The author describes several characteristics of the Nile grass rat that make this diurnal murid rodent an attractive laboratory animal.

Chromosomal and molecular characterization of Aethomys kaiseri from Zambia and Aethomys chrysophilus from Tanzania (Rodentia, Muridae)

Aethomys is a common and widespread rodent genus in the African savannas and grasslands. However, its systematics and taxonomy are still unclear as no study has covered the entire range. In fact it might not be a monophyletic genus and perhaps should be split into two subgenera, Micaelamys and Aethomys. In this paper, we present findings based on the cytogenetics and the entire cytochrome b sequence of two species from Zambia (A. kaiseri) and Tanzania (A. chrysophilus), and we compare them with the sequences of a South African species (A. namaquensis) and other allied muroid genera. Comparison of the banded chromosomes revealed complete G-band homology between the autosomes of the two species. However, the X and Y chromosomes clearly differ in size and in C- and G-banding, being much larger in A. kaiseri. Comparison of the cytochrome b sequences places the separation between A. kaiseri and A. chrysophilus at 4.49 Mya, a period of intense speciation in other African muroids. The resulting phylogeny strongly supports the idea of a paraphyletic group, suggesting the need to elevate the previously described subgenera to the genus rank.

Molecular analysis of populations of Ctenomys (Caviomorpha, Rodentia) with high karyotypic variability

The tuco-tucos (Ctenomys) are South American subterranean rodents that are some of the most chromosomally variable of all mammals. In this study we focus on Ctenomys of the "Corrientes species group" from that Argentine province and consisting of C. dorbignyi, C. perrensi, C. roigi and unnamed populations (Ctenomys sp.). A diploid range of 41-70 has been demonstrated for these taxa with multiple Robertsonian changes, pericentric inversions, heterochromatic modifications and other chromosomal rearrangements. To analyse the molecular variation in the Corrientes group, a 402 base pair fragment of mitochondrial cytochrome b was sequenced in 75 individuals from 26 populations. This generated 15 different haplotypes which were subjected to phylogenetic analysis. The different species within the Corrientes group failed to form monophyletic groups in the phylogenetic trees we generated and the divergences between haplotypes were low. Therefore, these molecular data demonstrate the recent subdivision of the Corrientes group with a substantial accumulation of chromosomal differences. Through our new chromosomal data and cytochrome b studies, we are able to subdivide the Ctenomys sp. populations into two groups and hypothesize on their relationships with the described Corrientes group species. Further studies are needed to establish the basis of the phenomenal chromosomal variation in this group.