Comparative cytogenetics of Chinese and Japanese raccoon dogs, Nyctereutes procyonoides

Evolution of MHC class I genes in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae)

Major histocompatibility complex (MHC) genes have been widely studied to assess the immunological fitness and evolutionary adaptation of animal populations. Among the Canidae, the raccoon dog's adventurous nature, omnivorous behavior, and high variability of intracellular pathogens make it ideal to study selection on MHC class I in a non-model canid species. Here, we examined allelic diversity and evolutionary patterns of MHC class I genes in the raccoon dog (Nyctereutes procyonoides). We identified 48 novel MHC class I alleles from 31 raccoon dogs from Japan and Russia. Some alleles were geographically restricted, whereas others were widely distributed across the species' range. The rate of non-synonymous substitutions was greater than that of synonymous substitutions for both exon 2 and exon 3 encoding α1 and α2 domains, respectively, in the α chain of the MHC class I protein. Positively selected sites at the amino acid level were evident in both the α1 and α2 domains, and a recombination breakpoint was found in exon 3. Bayesian phylogenetic trees showed no evidence of trans-species polymorphism (TSP) with alleles from carnivoran species in other families but did detect TSP between raccoon dogs and the domestic dog, Canis familiaris, indicative of long-term balancing selection in canids. Our results indicate that the extensive allelic diversity of MHC class I in Japanese and Russian raccoon dogs has been influenced and maintained by pathogen-driven positive selection, recombination, and long-term balancing selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13364-021-00561-y.

Molecular evolution of MHC class II DRB exon 2 in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae)

Raccoon dogs, Nyctereutes procyonoides, are native to East Asia, but have been introduced into western Russia and eastern Europe. To determine allelic diversity and elucidate the evolution of major histocompatibility complex (MHC) class II genes in the raccoon dog, we analysed a 237-bp region of DRB exon 2 from 36 individuals of native and introduced populations from Japan and Russia. We detected 23 DRB alleles (Nypr-DRBs), 22 of which were novel. Some alleles were found across the species’ range, while others were geographically restricted. For both native and introduced populations, the ratio of non-synonymous to synonymous substitution rates for codons at predicted antigen-binding sites was significantly greater than 2, indicating that Nypr-DRBs have evolved under positive selection. Mixed effect model evolution analysis and an algorithm to detect recombination showed five positively selected codons and one recombination breakpoint, respectively. Overall, our results suggest that the diversity of MHC class II DRB in N. procyonoides was influenced and maintained by recombination, pathogen-driven positive selection, geographical barriers and the founder effect. A Bayesian phylogenetic tree revealed no evidence of trans-species polymorphism (TSP), but instead showed monophyly for the Nypr-DRB alleles within a larger clade of canid sequences. The lack of TSP may have been due to long-term divergence of raccoon dogs from other canids, or to their having encountered different sets of pathogens due to occupying a different ecological niche.

Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes

B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation. Here, we used a similar approach to characterize Bs of the red fox (Vulpes vulpes L.) and the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray). We confirm the previous findings of the KIT gene on Bs of both species, but demostrate an independent origin of Bs in these species, with two reused regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates enrichment with cell-cycle genes, development-related genes, and genes functioning in the neuron synapse. The presence of B-chromosomal copies of genes involved in cell-cycle regulation and tissue differentiation may indicate importance of these genes for B chromosome establishment.

Genes on B chromosomes of vertebrates

BACKGROUND

There is a growing body of evidence that B chromosomes, once regarded as totally heterochromatic and genetically inert, harbor multiple segmental duplications containing clusters of ribosomal RNA genes, processed pseudogenes and protein-coding genes. Application of novel molecular approaches further supports complex composition and possible phenotypic effects of B chromosomes.

RESULTS

Here we review recent findings of gene-carrying genomic segments on B chromosomes from different vertebrate groups. We demonstrate that the genetic content of B chromosomes is highly heterogeneous and some B chromosomes contain multiple large duplications derived from various chromosomes of the standard karyotype. Although B chromosomes seem to be mostly homologous to each other within a species, their genetic content differs between species. There are indications that some genomic regions are more likely to be located on B chromosomes.

CONCLUSIONS

The discovery of multiple autosomal genes on B chromosomes opens a new discussion about their possible effects ranging from sex determination to fitness and adaptation, their complex interactions with host genome and role in evolution.

Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs

The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects.

Overwintering strategy of wild free-ranging and enclosure-housed Japanese raccoon dogs (Nyctereutes procyonoides albus)

The raccoon dog, Nyctereutes procyonoides, is a canid with a passive overwintering strategy in northern Europe. However, the behaviour and physiology of the Japanese subspecies, N. p. albus, which has fewer chromosomes than the other subspecies, remain unknown. We measured body temperature, body composition and blood biochemistry of wild free-ranging and fasted enclosure-housed N. p. albus during boreal winter in Hokkaido, Japan. Body temperature of N. p. albus decreased from 38 degrees C in autumn to 35.9-36.7 degrees C while maintaining a circadian rhythm in late February (n = 3). A transient 18-36% decrease in resting heart rate occurred when body temperature was low (n = 2). Despite a 33-45% decrease in body weight due to winter fasting, circulating glucose, total protein and triglyceride levels were maintained (n = 4). Serum urea nitrogen dropped by 43-45% from autumn to spring, suggesting protein conservation during fasting. The overwintering survival strategy of N. p. albus in central Hokkaido is based upon large changes in seasonal activity patterns, winter denning and communal housing without the large decrease in body temperature that is characteristic of subarctic animals exhibiting hibernation or torpor.

A canine X chromosome painting probe applied to four canid species: close relationship of a heterochromatic-like sequence between the dog and the blue fox

Microdissection of chromosomes is an invaluable tool to physically isolate single chromosomes, chromosome-arms or chromosome-bands and, subsequently generate painting probes with which numerical or structural aberrations of chromosomes can be studied. In addition, such painting probes can be used to compare karyotypic relationships among mammalian species. For the present study a canine whole X chromosome painting probe was prepared by means of conventional microdissection and degenerate-oligonucleotide-primed PCR. The application of this paint to the chromosomes of the domestic dog, red fox, blue fox and Chinese raccoon dog revealed hybridization to the entire X chromosome and the pseudo-autosomal region of the Y chromosome in all four species analysed. In the blue fox the same paint revealed additional strong hybridization signals on the heterochromatic arms after low-stringent posthybridization washes. The present study indicates the existence of an ancient canid heterochromatic-like DNA sequence, which survived in the proximal part of the X chromosome of all species studied and, in addition, was involved in the formation of heterochromatic arms in the blue fox.

Comparative chromosome painting defines the karyotypic relationships among the domestic dog, Chinese raccoon dog and Japanese raccoon dog

The Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54 + 2-3 B) and Japanese raccoon dog (Nyctereutes p. viverrinus, 2n = 38 + 3-4 B) are two subspecies of the same species. The genome-wide comparative chromosome map between the Japanese raccoon dog and domestic dog (Canis familiaris) has been established by fluorescence in-situ hybridization with a set of domestic dog painting probes. In this study, we established the comparative chromosome map for the Chinese raccoon dog and domestic dog. In total, dog probes specific for the 38 autosomes delineated 41 conserved chromosomal segments in the Chinese raccoon dog. Probes from dog chromosomes 1, 13 and 19 each painted two Chinese raccoon dog chromosome segments. Fifteen dog autosomal probes each hybridized to one Chinese raccoon dog chromosome, while each of the other dog autosomal probes painted to a single Chinese raccoon dog chromosomal arm. Dog X chromosome probe delineated the entire X chromosome of the Chinese raccoon dog; the dog Y chromosome probe hybridized to the pseudoautosomal region at the Xpter as well as the entire Y chromosome of the Chinese raccoon dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in the genomes of the Chinese and Japanese raccoon dogs demonstrates that their differences in the karyotypes of these two subspecies could have resulted from eight Robertsonian translocations. The large difference in chromosome number between the Chinese and Japanese raccoon dogs suggests that they should be considered as two distinct species.

Origin of human chromosome 2: an ancestral telomere-telomere fusion

We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG)n-(CCCTAA)m3'. Sequences flanking this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

On the robertsonian polymorphism found in the Japanese raccoon dog (Nyctereutes procyonoides viverrinus)

Karyotypes of 39 Japanese raccoon dogs (NPV) which appeared in the literature and of 7 previously unreported specimens were examined. Thirty four individuals showed the standard karyotype 2K = 26M + 10A + (M)X + (A)Y + Bs (2n = 38 + Bs), where Bs are supernumerary chromosomes. The remaining 11 individuals had 2K = 25M + 12A + XY + Bs (2n = 39 + Bs) and one was 2K = 23M + 16A + XY + Bs (2n = 41 + Bs). The G- and C-banding analyses of both somatic and germ cells revealed that these karyotypes with odd numbers are heterozygous (M/A) for a single Robertsonian rearrangement of chromosomes 2, 5, 6, 8, or 11, and one is M/A heterozygous for three autosomes: 5, 6, and 11.