Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae.
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ABSTRACT:
SUBMITTER: Vozdova M
PROVIDER: S-EPMC8465983 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Dictyocaulus species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or "husk"). There has been ongoing controversy surrounding the validity of some Dictyocaulus species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt) genomes of Dictyocaulus viviparus (from Bos taurus) with Dictyocaulus sp. cf. eckerti from red deer (Cervus elaphus), used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies. METHODS:The mt genomes were amplified from single adult males of D. viviparus and Dictyocaulus sp. cf. eckerti (from red deer) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), also employing data for other strongylids for comparative purposes. RESULTS:The circular mt genomes were 13,310 bp (D. viviparus) and 13,296 bp (Dictyocaulus sp. cf. eckerti) in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between D. viviparus and Dictyocaulus sp. cf. eckerti, and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both D. viviparus and Dictyocaulus sp. cf. eckerti were closely related, and grouped to the exclusion of selected members of the superfamilies Metastrongyloidea, Trichostrongyloidea, Ancylostomatoidea and Strongyloidea. CONCLUSIONS:Consistent with previous findings for nuclear ribosomal DNA sequence data, the present analyses indicate that Dictyocaulus sp. cf. eckerti (red deer) and D. viviparus are separate species. Barcodes in the two mt genomes and proteomes should serve as markers for future studies of the population genetics and/or epidemiology of these and related species of Dictyocaulus.
| S-EPMC3503548 | biostudies-literature
Project description:Blood samples were obtained from 38 wild red deer (Cervus elaphus) at two sites in Ireland and subjected to PCR analysis of the 18S rRNA gene followed by sequencing. Two fragments of the 18S rRNA gene were generated by two different PCR protocols and subsequent sequencing suggested that at least six of the deer were infected by a babesia that, in those loci, is indistinguishable from Babesia divergens, an important tick-borne pathogen of cattle and of zoonotic significance. Additionally, a B. odocoilei-like parasite was detected in three samples and a babesia that did not match any sequences in the GenBank database was found in five samples. Neither B. capreoli nor B. venatorum (EU1) were found. There have been several reports of B. divergens occurring in deer species, including red deer, roe deer (Capreolus capreolus) and reindeer (Rangifer tarandus). However, in view of recent re-sequencing of bovine-origin samples deposited previously in GenBank, it is unlikely that any of these sequences from deer are B. divergens. The present study describes the only deer piroplasm detected so far that shows complete identity with B. divergens, in just over half of the 18S rRNA gene. The entire gene of this deer parasite should be analysed and transmission experiments undertaken before the infectivity of B. divergens for red deer can be confirmed.
| S-EPMC3037898 | biostudies-literature
Project description:The presence of subcutaneous nodular onchocercosis was investigated at slaughter of 151 red deer (Cervus elaphus) (107 juveniles and 44 adults) between October-December 2015. The prevalence of subcutaneous nodules was 56%. Nodules were located in the lumbar region of the back in 96% of the cases, and 38% of the infected red deer had additional parasitic nodules in other body locations, such as rump, thorax, forelimbs and neck. The number of nodules per deer was 1-10 in two-thirds of the affected animals, and only 2% had more than 50 nodules. Significant differences in prevalence of nodule presence were found between adult (81%) and juvenile red deer less than two years of age (45%) (p = 0.0001). Species confirmation and identification was done on 14 randomly selected nodules taken from the lumbar region of 14 deer of different geographical origin, by sequencing the mitochondrial 12S, 16S and nad5 gene fragments. The sequences were more or less identical (12S = 99-100%; 16S = 93-100%; nad5 = 92-100%) to previously published sequences for Onchocerca flexuosa. The high prevalence of nodular onchocercosis caused by O. flexuosa in red deer in Sweden shows that the investigated areas in the southern third of Sweden have favorable vector (simuliids and ceratopogonids) conditions and suitable environment for the maintenance of the parasite. To our knowledge, this is the first systematic study of O. flexuosa in red deer in Sweden.
| S-EPMC5636018 | biostudies-literature
Project description:OBJECTIVES:Studying animal vocal aging has potential implication in the field of animal welfare and for modeling human voice aging. The objective was to examine, using a repeated measures approach, the between-year changes of weight, social discomfort score (bites of other hinds on hind pelt), body condition score (fat reserves) and acoustic variables of the nasal (closed-mouth) and the oral (open-mouth) contact calls produced by farmed red deer hinds (Cervus elaphus) toward their young. RESULTS:Repeated measures ANOVA revealed that with an increase of hind age for 1 year, the acoustic variables of their nasal contact calls (the beginning and maximum fundamental frequencies, the depth of frequency modulation and the peak frequency) decreased, whereas in their oral contact calls only the end fundamental frequency decreased. Duration and power quartiles did not change in any call type. Body weight and body condition score increased between years, whereas discomfort score decreased. Results of this study revealed directly the short-term effects of aging on the acoustics of the nasal contact calls in the same hinds. This study also confirmed that elevated emotional arousal during emission of the oral contact masks the effects of aging on vocalization in female red deer.
| S-EPMC6192103 | biostudies-literature
Project description:Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis-monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.
| S-EPMC8314804 | biostudies-literature
Project description:Melatonin is crucial in reproduction due its antioxidant, hormonal, and paracrine action. Melatonin membrane receptors (MT1/MT2) have been confirmed on spermatozoa from several species, but functionality studies are scarce. To clarify their role in ruminants as reproductive models, bull (Bos taurus, non-seasonal) and red deer (Cervus elaphus, highly seasonal) spermatozoa were analyzed after 4 h of incubation (38 °C, capacitating media) in 10 nM melatonin, MT1/MT2 agonists (phenylmelatonin and 8M-PDOT), and antagonists (luzindole and 4P-PDOT). Motility and functionality (flow cytometry: viability, intracellular calcium, capacitation status, reactive oxygen species (ROS) production, and acrosomal and mitochondrial status) were assessed. In bull, MT1 was related to sperm viability preservation, whereas MT2 could modulate cell functionality to prevent excess ROS produced by the mitochondria; this action could have a role in modulating sperm capacitation. Deer spermatozoa showed resistance to melatonin and receptor activation, possibly because the samples were of epididymal origin and collected at the breeding season's peak, with high circulating melatonin. However, receptors could be involved in mitochondrial protection. Therefore, melatonin receptors are functional in the spermatozoa from bull and deer, with different activities. These species offer models differing from traditional laboratory experimental animals on the role of melatonin in sperm biology.
| S-EPMC9181011 | biostudies-literature
Project description:Tarim red deer (Cervus elaphus yarkandensis) is the only subspecies of red deer (of 22 subspecies) from Central Asia. This species is a desert dweller of the Tarim Basin of southern Xinjiang, China, and exhibits some unique adaptations to the dry and extreme hot climate. We report here the assembly of a Tarim red deer genome employing a 10X Genomics library, termed CEY_v1. Our genome consisted of 2.6 Gb with contig N50 and scaffold N50 of 275.5 Kb and 31.7 Mb, respectively. Around 96% of the assembled sequences were anchored onto 34 chromosomes based on the published high-quality red deer genetic linkage map. More than 94% BUSCOs complete genes (including 90.5% single and 3.6% duplicated ones) were detected in the CEY_v1 and 20,653 genes were annotated. The CEY_v1 is expected to contribute to comparative analysis of genome biology, to evolutionary studies within Cervidae, and to facilitating investigation of mechanisms underlying adaptation of this species to the extreme dry and hot climate.
| S-EPMC7305323 | biostudies-literature
Project description:Most animals need to spend time being vigilant for predators, at the expense of other activities such as foraging. Group-living animals can benefit from the shared vigilance effort of other group members, with individuals reducing personal vigilance effort as group size increases. Behaviors like active scanning or head lifting are usually used to quantify vigilance but may not be accurate measures of this. We suggest that measuring an animal's blinking rate gives a meaningful measure of vigilance: increased blinking implies reduced vigilance, as the animal cannot detect predators when its eyes are closed. We describe an observational study of a captive population of red deer, where we measured the blinking rates of individual deer from groups of differing sizes (where mean group size ranged between 1 and 42.7 individuals). We demonstrate that as group size increases in red deer, individuals increase their blink rate, confirming the prediction that vigilance should decrease. Blinking is a simple non-invasive measure and offers a useful metric for assessing the welfare of animals experiencing an increase in perceived predation risk or other stressors.
| S-EPMC10015368 | biostudies-literature
Project description:(1) Background: Wild cervids play an important role in transmission cycles of tick-borne pathogens; however, investigations of tick-borne pathogens in sika deer in Germany are lacking. (2) Methods: Spleen tissue of 74 sympatric wild cervids (30 roe deer, 7 fallow deer, 22 sika deer, 15 red deer) and of 27 red deer from a farm from southeastern Germany were analyzed by molecular methods for the presence of Anaplasma phagocytophilum and Babesia species. (3) Results: Anaplasma phagocytophilum and Babesia DNA was demonstrated in 90.5% and 47.3% of the 74 combined wild cervids and 14.8% and 18.5% of the farmed deer, respectively. Twelve 16S rRNA variants of A. phagocytophilum were delineated. While the infection rate for A. phagocytophilum among the four cervid species was similar (71.4% to 100%), it varied significantly for Babesia between roe deer (73.3%), fallow deer (14.3%), sika deer (27.3%) and red deer (40.0%). Deer ≤2 years of age tested significantly more often positive than the older deer for both A. phagocytophilum and Babesia species. (4) Conclusions: This study confirms the widespread occurrence of A. phagocytophilum and Babesia species in wild cervids and farmed red deer in Germany and documents the co-occurrence of the two tick-borne pathogens in free-ranging sika deer.
| S-EPMC7699845 | biostudies-literature
Project description:The red deer is an intermediate feeder, showing a marked degree of forage selectivity, with seasonal morphological adaptations due to changes in food quality and availability. In captivity, deer have a limited choice of habitat and food, and we hypothesize that this condition affects the rumen environment. Rumen samples were collected from 20 farmed and 11 wild red deer in autumn 2018 in Poland, and analyzed for chemical composition, food residues, microbial population, and rumen papillation. Farmed deer had the highest Campylobacter spp., and total anaerobic bacteria, but lower Clostridium spp. Moreover, they showed a decrease in Diplodininae protozoa, and the presence of holotrichs that were absent in the wild animals. The rumen digesta of farmed animals had lower dry matter and acid detergent fiber than the wild ones. The analysis of food residues underlined the poor variety of the diet for animals in the farm. This apparently affected the papillation of the rumen, with animals of the farm having the shortest papillae of the Atrium ruminis. Overall, results suggest that red deer kept in farms, with a diet based mainly on grass, tree leaves, and some concentrate supplements, undergo a small modification of the rumen compared to the wild conspecifics.
| S-EPMC6769527 | biostudies-literature