Characteristics of the mitochondrial genome of Qinling zokor (Eospalax rufescens).
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ABSTRACT:
SUBMITTER: Song P
PROVIDER: S-EPMC7510645 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sequencing analysis of mitochondrial genomes is useful for understanding the genome structures. In this study, complete mitochondrial genomes of the Eospalax smithii was obtained by using next generation sequencing method. The complete mitogenome of E. smithii was 16,350 bp long, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region (D-loop). The overall base composition of the heavy strand is A (33.65%), C (23.80%), T (30.31%), and G (12.24%). The base compositions present highly biased toward A + T nucleotides. The result of phylogenetic analysis showed the five Eospalax species formed a monophyly with the high bootstrap value and as a sister group of the genus Myospalax. This is the first report of the complete mitochondrial genomes of E. smithii and the mitogenome is potentially important for evolutionary biology, population genetics, and species diagnosis studies of the Mysopalacinae.
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Project description:The ability to detect bitter tastes is important for animals; it can help them to avoid ingesting harmful substances. Bitter taste perception is mainly mediated by bitter taste receptor proteins, which are encoded by members of the Tas2r gene family and vary with the dietary preference of a specific species. Although individuals with different genotypes differ in bitterness recognition capability, little is known about the relationship between genetic variation and food selection tendencies at the intraspecific level. In this study, we examined the relationship between genotypes and diet in plateau zokor (Eospalax baileyi), a subterranean rodent endemic to the Qinghai-Tibet Plateau that caches food for the winter. We assayed the composition and taste profile of each plant contained in temporary caches and vicinity quadrats, which were representative of selected and available food, respectively. Bitter plant selection indices (E bitter) were estimated. We also sequenced 26 candidate Tas2r genes from zokors and determined their relationships with the E bitter of their caches. We identified four key results: (1) zokors varied considerably in both bitter food preference and Tas2r sequences; (2) five genes (zTas2r115,zTas2r119,zTas2r126,zTas2r134, and zTas2r136) exhibited allelic variation that was significantly associated with E bitter; (3) synonymous SNPs, nonsynonymous SNPs, and pseudogenization are involved in the genotype-phenotype relationship; (4) the minor genotypes of zTas2r115,zTas2r134, and zTas2r136 and the major genotypes of zTas2r119 and zTas2r126 cached more bitter plants. Our results link Tas2r variation with food selection behavior at the population level for the first time.
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Project description:The gonadotropins, luteinizing hormone (LH) and follicle stimulating hormone (FSH), are glycoprotein hormones in the hypothalamic-pituitary-gonadal (HPG) axis and regulate mammalian reproduction. The expression of these genes in the plateau zokor (Eospalax baileyi) is poorly understood. We characterized the immunolocalization of the luteinizing hormone receptor (LHR) and follicle stimulating hormone receptor (FSHR) in the testes and evaluated the positive immunohistochemical results and the relative mRNA expression of gonadotropin genes. During the non-breeding season (September), the relative testes weight and the seminiferous tubule diameter were significantly reduced. All germ cell types were observed during the breeding season (May), whereas only spermatogonia were observed during the non-breeding season. LHR was present in the Leydig cells whereas FSHR was present in the Sertoli cells. The mean optical density was higher during the breeding season. The mRNA expression of LHβ and FSHβ was lower in the pituitary but LHR and FSHR genes expression were higher in the testes during the breeding season. These data elucidate the expression of gonadotropin genes in the HPG axis of the male plateau zokor and suggest that gonadotropins play a vital role in the regulation of seasonal breeding.
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Project description:BACKGROUND: Protostrongylus rufescens is a metastrongyloid nematode of small ruminants, such as sheep and goats, causing protostrongylosis. In spite of its importance, the ecology and epidemiology of this parasite are not entirely understood. In addition, genetic data are scant for P. rufescens and related metastrongyloids. METHODS: The mt genome was amplified from a single adult worm of P. rufescens (from sheep) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of the mt genomes were concatenated and subjected to phylogenetic analysis using Bayesian inference. RESULTS: The circular mitochondrial genome was 13,619 bp in length and contained two ribosomal RNA, 12 protein-coding and 22 transfer RNA genes, consistent with nematodes of the order Strongylida for which mt genomes have been determined. Phylogenetic analysis of the concatenated amino acid sequence data for the 12 mt proteins showed that P. rufescens was closely related to Aelurostrongylus abstrusus, Angiostrongylus vasorum, Angiostrongylus cantonensis and Angiostrongylus costaricensis. CONCLUSIONS: The mt genome determined herein provides a source of markers for future investigations of P. rufescens. Molecular tools, employing such mt markers, are likely to find applicability in studies of the population biology of this parasite and the systematics of lungworms.
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Project description:Sexual dimorphism is prevalent in most living organisms. The difference in size between sexes of a given species is generally known as sexual size dimorphism (SSD). The magnitude of the SSD is determined by Rensch's rule where size dimorphism increases with increasing body size when the male is the larger sex and decreases with increasing average body size when the female is the larger sex. The unique underground environment that zokors (Eospalax baileyi) live under in the severe habitat of the Qinghai-Tibetan Plateau (QTP) could create SSD selection pressures that may or may not be supported by Rensch's rule, making this scientific question worthy of investigation. In this study, we investigated the individual variation between sexes in body size and SSD of plateau zokors using measurements of 19 morphological traits. We also investigated the evolutionary mechanisms underlying SSD in plateau zokors. Moreover, we applied Rensch's rule to all extant zokor species. Our results showed male-biased SSD in plateau zokors: The body- and head-related measurements were greater in males than in females. Linear regression analysis between body length, body weight, and carcass weight showed significant relationships with some traits such as skull length, lower incisor length, and tympanic bulla width, which might support our prediction that males have faster growth rates than females. Further, the SSD pattern corroborated the assumption of Rensch's rule in plateau zokors but not in the other zokor species. Our findings suggest that the natural underground habitat and behavioral differences between sexes can generate selection pressures on male traits and contribute to the evolution of SSD in plateau zokors.
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Project description:The Gansu zokor (Eospalax cansus), a typical subterranean rodent endemic to the Chinese Loess Plateau, spends almost its whole life in its self-constructed underground burrows and has strong adaptability to ambient hypoxia. Energy adaptation is the key to supporting hypoxia tolerance, and recent studies have shown that the intestinal microbiota has an evident effect on energy metabolism. However, how the gut microbiome of Gansu zokor will change in response to hypoxia and the metabolic role played by the microbiome have not been reported. Thus, we exposed Gansu zokors to severe hypoxia of 6.5% of O2 (6 or 44 h) or moderate hypoxia of 10.5% of O2 (44 h or 4 weeks), and then analyzed 16S rRNA sequencing, metagenomic sequencing, metagenomic binning, liver carbohydrate metabolites, and the related molecular levels. Our results showed that the hypoxia altered the microbiota composition of Gansu zokor, and the relative contribution of Ileibacterium to carbohydrate metabolism became increased under hypoxia, such as glycolysis and fructose metabolism. Furthermore, Gansu zokor liver enhanced carbohydrate metabolism under the short-term (6 or 44 h) hypoxia but it was suppressed under the long-term (4 weeks) hypoxia. Interestingly, under all hypoxia conditions, Gansu zokor liver exhibited enhanced fructose-driven metabolism through increased expression of the GLUT5 fructose transporter, ketohexokinase (KHK), aldolase B (ALDOB), and aldolase C (ALDOC), as well as increased KHK enzymatic activity and fructose utilization. Overall, our results suggest that the altered gut microbiota mediates the carbohydrate metabolic pattern under hypoxia, possibly contributing to the hepatic metabolic flexibility in Gansu zokor, which leads to better adaptation to hypoxic environments.
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Project description:In the present study, a new species of the genus Moniliformis species is described taxonomically in the mitochondrial genomic context. The parasite was found in a plateau zokor captured in a high-altitude area of Xiahe County of Gansu Province, China. The mitochondrial (mt) genome length of this new species was 14,066 bp comprising 36 genes and 2 additional non-coding regions (SNR and LNR), without atp8. The molecular phylogeny inferred by the cytochrome c oxidase subunit I gene (cox1) and the18S ribosomal RNA gene (18S rDNA) sequences showed that the parasite as a sister species to other Moniliformis spp. and was named Moniliformis sp. XH-2020. The phylogeny of the concatenated amino acid sequences of the 12 protein-coding genes (PCGs) showed Moniliformis sp. XH-2020 in the same cluster as Macracanthorhynchus hirudinaceus and Oncicola luehei confirming the cox1 and 18S rDNA phylogenetic inference. In addition, the entire mt genome sequenced in this study represents the first in the order Moniliformida, providing molecular material for further study of the phylogeny of the class Archiacanthocephala. Moreover, the species of this class, use arthropods as intermediate hosts and mammals as definitive hosts and are agents of acanthocephaliasis, a zoonosis in humans. Therefore, this study not only expands the host range among potential wild animal hosts for Archiacanthocephalans which is of great ecological and evolutionary significance but also has important significance for the research of zoonotic parasitic diseases.
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Project description:BackgroundSpecific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite's phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared the population genetics of the plateau zokor (Eospalax baileyi), a subterranean rodent, and its host-associated flea species, Neopsylla paranoma, with an aim to determine whether the two animals share a similar phylogeographic pattern.ResultsWe sampled 130 host-parasite pairs from 17 localities in the Qinghai-Tibet Plateau (QTP), China, and sequenced a mitochondrial DNA (mtDNA) segment (~2,500 bp), including the complete COI and COII genes. We also detected 55 zokor and 75 flea haplotypes. AMOVA showed that the percentage of variation among the populations of zokors constituted 97.10%, while the within population variation was only 2.90%; for fleas, the values were 85.68% and 14.32%, respectively. Moreover, the flea Fst (fixation index) values were significantly smaller than in zokor. Although the Fst values between zokors and fleas were significantly and positively correlated (N=105, R=0.439, p=0.000), only a small amount (R2=0.19) of the flea Fst variations could be explained by the zokor Fst variations. The two animals showed very distinct haplotype network structures from each other while co-phylogenetic analyses were unable to reject the hypothesis of an independence of speciation events.ConclusionsZokors and fleas have very distinct population genetic patterns from each other, likely due to the influence of other sympatrically-distributed vertebrates on the transmission of fleas.
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Project description:Zokors in the genus Eospalax, which are endemic to northern and western China, are subterranean rodents that inhabit various niches, including grasslands, high-altitude meadows, forests, and farmlands. Six species in Eospalax were described a century ago but their taxonomy and phylogeny remain controversial. In this study, we performed high-depth whole-genome sequencing of 47 zokor samples, comprising all six previously described species. Genomic analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named species. According to the inferred phylogenetic relationships, Eospalax first divergent into two clades in the early Pliocene (ca. 4.68 million years ago (Ma)), one inhabiting the high-altitude Qinghai-Xizang (Tibet) Plateau (QTP) and adjacent regions, and the another inhabiting the low-altitude Loess Plateau and Qinling-Daba Mountains. The most recent divergences occurred between E. baileyi and E. smithii and between E. rufescens and E. rothschildi in the late Pliocene (ca. 2.09 and 2.19 Ma, respectively). We also collected specimens of zokors in the southern Hengduan Mountains (Muli County, Sichuan Province), far from the known distributions of all other zokors. Morphological and molecular analyses strongly suggested that the specimens represent a new species, formally described here as Eospalax muliensis sp. nov. The new species belongs to the high-altitude clade and diverged from closely related species (ca. 4.22 Ma) shortly after the first divergence in Eospalax. Interestingly, Eospalax muliensis sp. nov. possesses more supposedly plesiomorphic characters, suggesting a possible origin of the genus in the Hengduan Mountains.
| S-EPMC9113976 | biostudies-literature
Project description:The complete mitochondrial genome (mitogenome) sequence of Achalinus rufescens was determined by using a PCR-based method. The total length of mitogenome is 17,339 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (D-loop). All the protein-coding genes of A. rufescens were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of A. rufescens and 11 other closely species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of A. rufescens.
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