Development of a tetra-primer ARMS-PCR for identification of sika and red deer and their hybrids

Accurate identification of deer-derived components is significant in food and drug authenticity. Over the years, several methods have been developed to authenticate these products; however, identifying whether female deer products are hybrids is challenging. In this study, the zinc finger protein X-linked (ZFX) gene sequences of sika deer (Cervus nippon), red deer (Cervus elaphus) and their hybrid offspring were amplified and sequenced, the X221 and X428 species-specific single nucleotide polymorphisms (SNP) loci were verified, and a tetra-primer amplification refractory mutation system (T-ARMS-PCR) assay was developed to identify the parent-of-origin of female sika deer, red deer, and their hybrid deer. The T-ARMS-PCR developed based on the X221 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 486 bp, 352 bp, and 179 bp, respectively, just as X428 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 549 bp, 213 bp, and 383 bp, respectively. Forty products labeled deer-derived ingredients randomly purchased were tested using this assay, and the results showed that the identification results based on the two SNP loci were utterly consistent with the actual sources. In addition, this method was found to be accurate, simple, convenient, and with high specificity, thus providing an essential technical reference for deer product species identification. It is also an important supplement to the identification methods of the original ingredients of existing deer products.

Molecular identification of Sarcocystis species in sika deer (Cervus nippon) of free-ranging populations in Germany and Austria

In this study, for the first time, Sarcocystis species were identified molecularly in sika deer (Cervus nippon) that form free-ranging populations in several countries of Europe. Diaphragm muscle samples from 151 deer from 10 populations in Germany and Austria were examined for sarcocysts. By one-gram methylene-blue staining, sarcocysts were recorded in samples of 114 animals (75.5%) which originated from all populations. Sarcocysts were more often (p < 0.0001) recorded in yearling and adult deer than in calves. Infection intensity was generally low with ~ 70% of the sarcocyst positive deer harbouring ≤ 10 sarcocysts per 1-gram diaphragm muscle. Based on cox1 sequence comparison, 10 species of Sarcocystis, all previously reported parasitizing cervids, were identified: S. elongata, S. entzerothi, S. hjorti, S. iberica, S. japonica, S. linearis, S. morae, S. pilosa, S. silva and S. truncata. The prevailing S. hjorti was detected in sika deer of all 10 populations. The identification in sika deer of S. hjorti, S. iberica, S. elongata, S. linearis, S. morae and S. silva constitutes new host records. With the additional species records of this study, the highest number of Sarcocystis species, at least 16, was identified in this host.

Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution

Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.

First Detection and Molecular Identification of Entamoeba bovis in Farm-Raised Sika Deer from Anhui Province, China

BACKGROUND

Protozoans of Entamoeba spp. are one of the most common enteric parasites that infect humans and diverse animals including deer.

PURPOSE

However, data regarding the prevalence and species/genotypes of Entamoeba spp. in deer in China is scarce. This study investigated the prevalence and species distribution of Entamoeba spp. in sika deer (Cervus nippon) in Anhui Province.

METHODS

In our survey, 336 fecal samples were collected from five sika deer farms in different regions of Anhui Province. All samples were examined for the presence of Entamoeba spp. by PCR and phylogenetic analysis of the conserved 18S rRNA gene.

RESULTS

106/336 (31.5%) fecal samples were positive for Entamoeba spp. A statistically significant difference in the prevalence of Entamoeba spp. infection was observed between sampling farms (p < 0.001), and the prevalence of Entamoeba spp. in male and female sika deer showed no significant difference (p > 0.05). Sequence and phylogenetic analysis revealed the single species, E. bovis, was identified in this study.

CONCLUSION

This is the first report about the identification of E. bovis in farm-raised sika deer in China, and these results expand our understanding of host range and species distribution of Entamoeba spp. in ruminants.

The first high-quality reference genome of sika deer provides insights for high-tannin adaptation

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

Distribution, prevalence, and intensity of Sarcocystis infections in sika deer (Cervus nippon) of free-ranging populations in Germany and Austria

Sika deer (Cervus nippon), which are native to the Japanese islands and the adjacent mainland of eastern Asia, have been introduced into Europe and established free-ranging populations in several countries. Various Sarcocystis species have been identified recently from farmed "mainland sika" deer in Lithuania and native "Japanese sika" deer in Japan. To study the distribution, prevalence and intensity of Sarcocystis infection in free-ranging sika deer outside of their natural range heart and/or diaphragm samples of 311 animals from nine populations in Germany and Austria were examined by histology.Overall, sarcocysts were detected in either heart or diaphragm of 107/311 deer (34.4%) with prevalence ranging roughly from 5 to 50% among the populations. Considering the 263 animals with both heart and diaphragm available, prevalence varied significantly (p < 0.0001) among calves (20.2%), yearlings (40.3%), and adult deer (49.1%) but did not differ between male and female deer (48.3% vs. 43.7%; p = 0.6483). Occurrence of sarcocysts in heart vs. diaphragm indicated a marginal difference (27.8% vs. 20.9%; p = 0.0839). Intensity of infection in all but one heart positive and all diaphragm positive animals was low (< 10 sarcocysts per square centimeter muscle cut). While heart sarcocyst counts of yearlings and adult deer were higher than those of calves and were higher in male compared to female sika deer, diaphragm sarcocyst counts did not differ significantly between age groups and sexes. Sarcocystis infection was demonstrated at variable prevalence in sika deer in all populations but intensity is apparently low. Further studies are needed to identify the species of Sarcocystis infecting sika deer naturalized outside their natural range.

Identification of hepatitis E virus in wild sika deer in Japan

Hepatitis E virus (HEV) is a zoonotic agent mainly transmitted through the consumption of uncooked or undercooked meat products derived from infected animals. In Japan, domestic pigs and wild boars are the major animal reservoirs, and whether or not deer are an HEV reservoir remains controversial. We analyzed 395 serum and 199 liver samples from 405 sika deer (Cervus nippon) caught in the wild between 1997 and 2020 in 11 prefectures of Japan for markers of HEV infection. Overall, 17 deer had anti-HEV IgG (4.3%), while 1 (0.2%) had HEV RNA (genotype 3b), indicating the occurrence of ongoing HEV infection in wild deer in Japan. An analysis of the complete HEV genome (deJOI_14) recovered from a viremic deer in Oita Prefecture revealed only 88.8% identity with the first HEV strain in sika deer (JDEER-Hyo03L) in Japan, being closest (96.3%) to the HEV obtained from a hepatitis patient living in the same prefecture. Of note, the deJOI_14 strain was 8.7-9.0% different from the wild boar HEV strains obtained in the same habitat and the same year, suggesting that difference in infected HEV strains between boar and deer may be explained by the limited possibility of close contact with each other, although boars are a known source of HEV infection. Increased numbers of hepatitis E cases after consumption of raw or undercooked meat products of wild deer have been reported in Japan. These results suggest a low but nonnegligible zoonotic risk of HEV infection in wild deer in this country.

Helminthes detected from wild sika deer (Cervus nippon centralis) in Kanto-Chubu region, Japan

The helminth fauna of 105 sika deer (Cervus nippon centralis) captured in Yamanashi, Kanagawa and Nagano Prefectures, Japan was investigated during 2014-2019. As a result, 12 helminthes, i.e. 3 digeneans (Ogmocotyle sikae, Dicrocoelium chinensis and D. dendriticum), 8 nematodes (Gongylonema pulchrum, Dictyocaulus sp., Pygarginema sp., Spiculopteragia houdemeri, Chabaudstrongylus ninhae, Trichuris discolor, Oesophagostomum sikae and Oes. asperum), and 1 cestode (Moniezia sp.) were detected. To our knowledge, this is the first report of Pygarginema sp., Cha. ninhae, and Oes. asperum from sika deer in Japan. Some helminthes detected in the present study can infect livestock. Considering the possibility of the spread of the helminthes to livestock through deer excrement, it is important to promote understanding the parasite fauna in wild deer.

Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip

Background

China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required.

Results

In this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources.

Conclusion

We successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-00994-z.

Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network

The growth of antler is driven by endochondral ossification in the growth center of the apical region. Antler grows faster than cancer tissues, but it can be stably regulated and regenerated periodically. To elucidate the molecular mechanisms of how antler grows rapidly without carcinogenesis, in this study, we used RNA-seq technology to evaluate the changes of miRNA and mRNA profiles in antler at four different developmental stages, including 15, 60, 90, and 110 days. We identified a total of 55004 unigenes and 246 miRNAs of which, 10182, 13258, 10740 differentially expressed (DE) unigenes and 35, 53, 27 DE miRNAs were identified in 60-day vs. 15-day, 90-day vs. 60-day, and 110-day vs. 90-day. GO and KEGG pathway analysis indicated that DE unigenes and DE miRNA were mainly associated with chondrogenesis, osteogenesis and inhibition of oncogenesis, that were closely related to antler growth. The interaction networks of mRNA-mRNA and miRNA-mRNA related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler were constructed. The results indicated that mRNAs (COL2A1, SOX9, WWP2, FGFR1, SPARC, LOX, etc.) and miRNAs (miR-145, miR-199a-3p, miR-140, miR-199a-5p, etc.) might have key roles in chondrogenesis and osteogenesis of antler. As well as mRNA (TP53, Tpm3 and ATP1A1, etc.) and miRNA (miR-106a, miR-145, miR-1260b and miR-2898, etc.) might play important roles in inhibiting the carcinogenesis of antler. In summary, we constructed the mRNA-mRNA and miRNA-mRNA regulatory networks related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler, and identified key candidate mRNAs and miRNAs among them. Further developments and validations may provide a reference for in-depth analysis of the molecular mechanism of antler growth without carcinogenesis.

Bovine Tuberculosis: The Emergence of a New Wildlife Maintenance Host in Ireland

Despite advances in herd management, tuberculosis (TB) continues to affect ~0. 5% of Ireland's national cattle herd annually. It is clear that any "final" eradication of TB in cattle will need to address all TB maintenance hosts in the same environment. In Ireland and the UK, European Badgers (Meles meles) are a known TB maintenance host, while deer are recognised as spillover hosts. However, deer have been identified as maintenance hosts in other countries and Sika deer, specifically, have been identified with TB in Ireland. We examined the power of cattle, badger and Sika deer densities (at the county level) to predict cattle TB-breakdowns in Ireland, at both the herd and the individual level, using data collected between 2000 and 2018. Our hypothesis was that any positive correlations between deer density and cattle TB-breakdowns would implicate deer as TB maintenance hosts. Using linear multiple regressions, we found positive correlations between deer density and cattle TB-breakdowns at both the herd and individual levels. Since Sika deer in County Wicklow are known to have TB, we ran further regressions against subsets of data which excluded individual Irish counties. Analyses excluding Wicklow data showed much weaker correlations between Sika deer density and cattle TB-breakdowns at both the herd and individual levels, suggesting that these correlations are strongest in County Wicklow. A similar effect for badger density was seen in County Leitrim. While locally high densities of Sika deer persist in Irish counties, we believe they should be considered an integral part of any TB-control programme for those areas.

Molecular detection of Blastocystis in black bears and sika deer in northern China

Protists of the Blastocystis genus are distributed worldwide and can infect a range of hosts. However, data concerning Blastocystis infection are limited for sika deer and are not available for black bears. Therefore, in the present study, a total of 312 black bears (Ursus thibetanus) from Heilongjiang Province and 760 sika deer (Cervus nippon) from four different northern Chinese provinces were investigated. Blastocystis infection in these animals was detected via PCR amplification of the small subunit rRNA gene in fecal samples. The prevalence of Blastocystis infection in black bears and sika deer was 14.4% (45/312 positive samples) and 0.8% (6/760 positive samples), respectively. Young black bears (18.3%) had a significantly higher Blastocystis prevalence than adult bears (9.1%). The prevalence of Blastocystis was significantly higher in black bears raised outdoors (24.6%) than in bears raised indoors (12.2%). Blastocystis-positive sika deer were only found in Jilin Province (1.3%, 6/480). Female sika deer (0%, 0/61) had a significantly lower Blastocystis prevalence than males (0.9%, 6/699). Sanger sequencing was used to determine the small subunit rRNA gene sequences of the Blastocystis-positive PCR products. A neighbor-joining phylogenetic tree based on the small subunit rRNA gene sequences showed that only Blastocystis subtype (ST)1 was identified in black bears, whereas ST10 and ST14 were found in sika deer. This is the first report of Blastocystis ST1 infection in black bears. These findings also extend the distribution information of Blastocystis subtypes, which will provide a foundation for further study of Blastocystis in different hosts in China.

Lipoptena fortisetosa as a vector of Bartonella bacteria in Japanese sika deer (Cervus nippon)

Background

Two species of deer ked (Lipoptena cervi and L. mazamae) have been identified as vectors of Bartonella bacteria in cervids in Europe and the USA. In an earlier study we showed that Japanese sika deer (Cervus nippon) harbor three Bartonella species, namely B. capreoli (lineage A) and two novel Bartonella species (lineages B and C); however, there is currently no information on the vector of Bartonella bacteria in sika deer. The aim of this study was to clarify potential vectors of Bartonella in Japanese sika deer.

Methods

Thirty-eight wingless deer keds (L. fortisetosa) and 36 ticks (Haemaphysalis and Ixodes species) were collected from sika deer. The prevalence of Bartonella in the arthropods was evaluated by real-time PCR targeting the 16S−23S internal transcribed spacer (ITS) and by culture of the organisms. The total number of Bartonella bacteria were quantified using real-time PCR. The distribution of Bartonella bacteria in deer ked organs was examined by immunofluorescence analysis. The relationship of Bartonella strains isolated from sika deer and arthropods were examined by a phylogenetic analysis based on concatenated sequences of the gltA, rpoB, ftsZ, and ribC genes, followed by a BLAST search for gltA and rpoB.

Results

Bartonella prevalence in deer keds was 87.9% by real-time PCR and 51.5% in culture and that in the ticks was 8.3% by real-time PCR and 2.8% in culture. The mean number of Bartonella bacteria per ked was calculated to be 9.2 × 10⁵ cells. Bartonella aggregates were localized in the midgut of the keds. The phylogenetic analysis and BLAST search showed that both the host deer and the keds harbored two Bartonella species (lineages B and C), while B. capreoli (lineage A) was not detected in the keds. Two novel Bartonella species (lineages D and E) were isolated from one ked.

Conclusions

Lipoptena fortisetosa likely serves as a vector of at least two Bartonella species (lineages B and C), whereas ticks do not seem to play a significant role in the transmission of Bartonella between sika deer based on the lower detection rates of Bartonella in ticks compared to keds. Bartonella species in lineages D and E appear to be L. fortisetosa-specific strains.

Occurrence of the giant liver fluke, Fascioloides magna, in sympatric wild ungulates in one area in the Upper Palatinate Forest (northeastern Bavaria, Germany)

Associated with the spreading in (north)western direction of Fascioloides magna from its historic endemic area in Bohemia with its cervid hosts, unusual noticeable hepatic lesions (black-colored tissue, hemorrhage) were observed in deer harvested in hunting grounds and one deer farm located in the Upper Palatinate Forest close to the border to the Czech Republic, initially in the years of 2007 and 2009, respectively. Confirmation of the suspected diagnosis of F. magna infection in October 2011 prompted investigations on the occurrence of "fascioloidosis" among wild ungulates in that locality. From October 2011 to January 2014, livers from 89 cervids and two wild boars were examined for flukes. Thirty-seven livers (40.6%) harbored F. magna: 17 of 21 red deer, nine of 24 sika deer, six of eight fallow deer, four of 36 roe deer, one of two wild boars. Fluke burdens ranged from 2 up to 151 in red deer, from 2 up to 37 in fallow deer, and from 1 up to 7 in sika deer and in roe deer; one fluke was recovered from the liver of one wild boar. No other parasites were recovered from the livers. The rate of recovery of F. magna differed significantly (p < 0.001) among the species of deer (red deer, 81.0%; sika deer, 37.5%; fallow deer, 75.0%; roe deer, 11.1%) and between the age groups (< 1 year: 22.2%, 1 to 2 years: 26.0%, and > 2 years: 70.0%, respectively). There was no association (p > 0.1) between the rate of recovery of F. magna and the sex of the combined 80 deer of ≥ 1 year of age (male: 41.8% and female: 31.4%). The occurrence of F. magna in the wild ungulates in the Upper Palatinate Forest area in northeastern Bavaria is of epidemiological importance for the further spreading of the parasite into Germany with migrating deer.

Utilizing attached hard ticks as pointers to the risk of infection by Babesia and Theileria species in sika deer (Cervus nippon yesoensis), in Japan

Ticks are hematophagous ectoparasites that have a significant impact on their animal hosts. Along with mosquitoes, they are the main arthropod vectors of disease agents in domestic animals, wildlife and humans. To investigate the occurrence and prevalence of piroplasmids in ticks, DNA was extracted from 519 hard ticks collected from 116 hunted Hokkaido sika deer (Cervus nippon yesoensis). The success of the DNA extraction was confirmed by touchdown PCR targeting the mitochondrial 16S rDNA gene of ticks. Touchdown PCR and reverse line blot (RLB) hybridization targeting the 18S rRNA gene were used to detect 14 piroplasm species. All hard ticks parasitizing Hokkaido sika deer were identified as belonging to the genera Ixodes and Haemaphysalis. In total 163 samples (31.4%) were positive for Babesia and Theileria spp. among tick species according to RLB hybridization. Tick DNA hybridized to the oligonucleotide probes of Theileria sp. Thrivae (27.0% of ticks; 140/519), Theileria capreoli (10.6%; 55/519), Babesia divergens-like (1.7%; 9/519), Babesia sp. (Bab-SD) (0.6%; 3/519), Babesia microti U.S. (0.4%; 2/519), and B. microti Hobetsu (0.4%; 2/519). The partial sequencing and phylogenetic analyses of the 18S rRNA gene confirmed the RLB hybridization results. Further investigations are needed to reveal the epidemiology and respective vectors of these pathogens.

Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer

BACKGROUND

Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler.

RESULTS

We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027.

CONCLUSIONS

This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.

Reduction in the Radiocesium in Meats of the Sika Deer and Wild Boar by Cooking

ABSTRACT

The behavior of radiocesium in wild animal meats upon cooking was investigated. The ratio of the concentration change (processing factor, Pf), remaining ratio (food processing retention factor, Fr), and removal ratio of radiocesium in the meats by grilling, boiling, and steaming were determined. Differences in cooking methods, rather than differences in meat parts or animal species, clearly influenced the Pf, Fr, and removal ratios. The mean Fr values were 0.9 (range, 0.7 to 1.0) for grilling, 0.6 (range, 0.4 to 0.7) for boiling, and 0.5 (range, 0.4 to 0.7) for steaming. The removal effect of grilling (11%) was lower than that of boiling (41%) or steaming (47%). The mean value of Pf was 1.2 (range, 1.1 to 1.6) for grilling, 0.8 (range, 0.6 to 0.9) for boiling, and 0.8 (range, 0.7 to 1.0) for steaming. The radiocesium concentration in the meats increased only upon grilling, but not by boiling or steaming. This difference is due to the lower removal effect of grilling than that of boiling and steaming. Therefore, boiling and steaming were more effective than grilling for removing radiocesium and reducing its concentration in wild animal meats. Furthermore, the ratio of water content fluctuations due to boiling was negatively correlated with Pf and Fr. It was evident that greater reductions in water content resulted in lower concentrations and improved radiocesium removal in the meats. These results suggest that some of the radiocesium naturally present in the meats is soluble in water and that the radiocesium dissolved in water can be removed from the meat with the release of water from the tissue.

HIGHLIGHTS

Molecular detection of Cryptosporidium and Enterocytozoon bieneusi in dairy calves and sika deer in four provinces in Northern China

The protistan pathogens Cryptosporidium and Enterocytozoon bieneusi can cause significant intestinal diseases in animals and humans. However, limited information is available regarding prevalence and molecular characterization of Cryptosporidium and E. bieneusi in ruminants in Northern China. In this study, the overall prevalence of Cryptosporidium and E. bieneusi was 19.3% (62/321) and 28.97% (93/321) in dairy calves and 1.10% (9/818) and 13.57% (111/818) in sika deer (Cervus nippon) in four provinces in Northern China, respectively. The prevalence of Cryptosporidium and E. bieneusi in different factor groups was various. Five Cryptosporidium species/genotypes were identified, of which C. parvum, C. ryanae, C. bovis, and C. andersoni were only found in dairy calves, and only Cryptosporidium deer genotype was found in sika deer. Moreover, J, I, and BEB4 ITS genotypes of E. bieneusi were found in dairy calves, and six known genotypes (JLD-III, JLD-IX, JLD-VII, EbpC, BEB6, and I) and ten novel genotypes (namely LND-I and JLD-XV to JLD-XXIII) were found in sika deer in this study. Cryptosporidium parvum and E. bieneusi genotype J were identified as the predominant species/genotypes in dairy calves, whereas the predominance of Cryptosporidium spp. and E. bieneusi in sika deer was Cryptosporidium deer genotype and BEB6, respectively. The present study reported the prevalence and genotypes of Cryptosporidium and E. bieneusi in dairy calves and sika deer in four provinces in northern China. The present findings also suggest that investigated dairy calves and sika deer may play an important role in the transmission of E. bieneusi and Cryptosporidium to humans and other animals, and also in an effort to better understand the epidemiology of these enteric pathogens in China.

Plant community recovery from intense deer grazing depends on reduction of graminoids and the time after exclosure installation in a semi-natural grassland

Exclosures that exclude large herbivores are effective tools for the protection and restoration of grazed plant communities. However, previous studies have shown that the installation of an exclosure does not ensure plant community recovery. Our study aimed to determine the effects of the domination of unpalatable plants and the timing of exclosure installation on the plant community recovery process in montane grassland overgrazed by sika deer (Cervus nippon) in Japan. In this study we compared plant species composition and their cover with inside and outside exclosures installed at different times. Furthermore, we also compared them with those in 1981, when density of sika deer was very low. We used quadrats inside and outside fenced areas established in 2010 and 2011 to record both the cover and the height of species in each quadrat between 2011 and 2015. Plant cover, with the exception of graminoid species, increased in later years in all treatments. Non-metric multidimensional scaling (NMDS) plots showed significantly differentiated treatment trends. The species composition within the 2010 fenced area gradually shifted to greater similarity with the species composition reported in 1981. The plant community in the 2011 fenced area was slower to recover. Compositions of plant communities outside the fenced areas hardly changed from 2011 to 2015. Chao’s dissimilarity index decreased over time between the plant community surveyed between 2011 and 2015 and the past plant community in 1981 within the exclosures, and was higher in the 2011 fenced area than in the 2010 fenced area. In conclusion, we show that the reduction of graminoids and the time after exclosure installation were important for plant community recovery from deer grazing damage. A delay in exclosure installation of one year could result in a delay in plant community recovery of more than one year.

Malignant catarrhal fever: An emerging yet neglected disease in captive sika deer (Cervus nippon) herds in China

Malignant catarrhal fever (MCF) is a fatal lymphoproliferative disease that represents a serious problem in the deer-rearing industry. To better understand an MCF-like disease that has emerged in northern China since 2015, we investigated ten cases by documenting clinical and epidemiological data and analysing causative agents and histopathological changes. In addition, a retrospective screen for Macavirus DNA and a questionnaire-based survey were conducted. Epizootic MCF in Chinese sika deer herds has emerged with a low morbidity of 3.8% (95% CI: 2.5%-5.1%) and a high mortality of 93.2% (95% CI: 86.6%-99.9%). The disease course varied from 3 to 12 days. Aetiologically, OvHV-2 was predominant in the MCFV, accounting for most MCF cases (21/23). In contrast, only two CpHV-2 isolates were phylogenetically closely related to CpHV-2. Diarrhoea and nasal discharges were the most frequent manifestations, although clinical signs varied in some cases. Pathologically typical lesions of haemorrhage, necrosis and lymphoid cell infiltration were readily observed in a variety of organs. Vasculitis caused by vascular and perivascular lymphoid cell infiltration was common. The retrospective survey suggested a low positive rate (3/275) of MCFV DNA in peripheral blood lymphocytes (PBL). The questionnaire-based survey suggested the disease was neglected by local veterinarians, who did not acknowledge the risk of co-rearing deer with reservoir species. Collectively, the emerging epizootic MCF in Chinese sika deer herds remains neglected, emphasizing the urgency of initiating full-field diagnoses and control strategies.

Molecular authentication of sika deer (Cervus nippon) based on allele-specific PCR

Sika deer (Cervus nippon) is listed as a tonic in many ancient Chinese pharmaceutical. Many adulterants of sika deer products have been found in Chinese medicinal materials markets, which led to detrimental impacts in clinical treatment. However, it is lack of the rapid and effective identification method for sika deer. This study amplified 574 bp fragment of mtDNA COI region of 19 samples from seven Cervidae species, and the relevant five sequences from reindeer (Rangifer tarandus) were downloaded from GenBank. It was found that there were two SNP loci for sika deer. Phylogenetic analysis indicated that individuals from sika deer clustered together. Based on SNP locus, one pair specific primer for allele-specific PCR identification of sika deer was designed, which could be used to rapidly and accurately identify sika deer.

The effects of CRISPR-Cas9 knockout of the TGF-β1 gene on antler cartilage cells in vitro

Background

Deer antler is the only mammalian organ that can be completely regenerated every year. Its periodic regeneration is regulated by multiple factors, including transforming growth factor β (TGF-β). This widely distributed multi-functional growth factor can control the proliferation and differentiation of many types of cell, and it may play a crucial regulatory role in antler regeneration. This study explored the role of TGF-β1 during the rapid growth of sika deer antler.

Methods

Three CRISPR-Cas9 knockout vectors targeting the TGF-β1 gene of sika deer were constructed and packaged with a lentiviral system. The expression level of TGF-β1 protein in the knockout cell line was determined using western blot, the proliferation and migration of cartilage cells in vitro were respectively determined using EdU and the cell scratch test, and the expression levels of TGF-β pathway-related genes were determined using a PCR array.

Results

Of the three gRNAs designed, pBOBI-gRNA2 had the best knockout effect. Knockout of TGF-β1 gene inhibits the proliferation of cartilage cells and enhances their migration in vitro. TGF-β signaling pathway-related genes undergo significant changes, so we speculate that when the TGF-β pathway is blocked, the BMP signaling pathway mediated by BMP4 may play a key role.

Conclusions

TGF-β1 is a newly identified regulatory factor of rapid growth in sika deer antler.

Seroprevalence of Toxoplasma gondii in wild sika deer in Japan

Toxoplasmosis is a food-borne infection that is widespread around the world, causing congenital disorders and opportunistic infections. Ingestion of undercooked meat is one of the risk factors for infection with the causative agent, Toxoplasma gondii. Japanese people occasionally eat rare meat as a traditional cuisine style called "Sashimi". A rapid increase in venison consumption in Japan has occurred mainly due to enhanced population control of wild Japanese deer (Cervus nippon) in recent decades. In particular, Yezo-sika deer (C. n. yesoensis) in Hokkaido (the northernmost and largest prefecture in Japan) is frequently supplied to markets as branded game/bushmeat. To study the possible burden of Toxoplasma gondii among wild Yezo-sika deer, plasma samples of Yezo-sika deer hunted during two seasons, 2010-2012, in Eastern Hokkaido were investigated. A total 80 samples were examined using the Sabin-Feldman dye test, which is highly specific and sensitive for identifying the development and persistence of antibodies after primary Toxoplasma infection, demonstrating that 38 cases (47.5%) were seropositive (cut-off titer <1:16). Antibody prevalence of T. gondii in female deer was higher than in males. Adult deer aged 3 years or over showed higher seroprevalence compared with younger animals. The overall seroprevalence fluctuated significantly according to the season when the deer were hunted. These results indicated widespread infection of T. gondii among Japanese wild Yezo-sika deer, suggesting that both appropriate handling and treatment of bushmeat are required to prevent food-borne toxoplasmosis in Japan.

Genome-wide DNA methylation analysis of the regenerative and non-regenerative tissues in sika deer (Cervus nippon)

Deer antlers, the secondary organs of deer, are a unique model to study regeneration of organ/tissue in mammals. Pedicle periosteum (PP) is the key tissue type for antler regeneration. Based on our previous study, the DNA methylation was found to be the basic molecular mechanism underlying the antler regeneration. In this study, we compare the genome-wide DNA methylation level in regenerative tissues (the potentiated PP of antler, muscle, heart and liver) and non-regenerative tissue (the dormant PP) of deer by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) method. Our results showed that DNA methylation level was significantly lower in the regenerative tissues compared to the non-regenerative tissue (P < 0.05). Furthermore, 26 T-DMRs which displayed different methylated status in regenerative and non-regenerative tissues were identified by the MSAP method, and were further confirmed by Southern blot analysis. Taken together, our data suggest that DNA methylation, an important epigenetic regulation mechanism, may play an important role in the mammalian tissue/organ regeneration.

from the sika deer (Cervus nippon), including two new species Sarcocystis frondea and Sarcocystis nipponi

Diaphragm muscles of 25 sika deer (Cervus nippon) farmed in Lithuania were examined for sarcocysts of Sarcocystis species. Two new Sarcocystis species, Sarcocystis frondea and Sarcocystis nipponi, were observed using light microscopy (LM) and transmission electron microscopy (TEM) and characterized by 18S ribosomal DNA (rDNA) and subunit I of cytochrome c oxidase (cox1) sequence analyses. By LM, sarcocysts of S. frondea and S. nipponi were ribbon-shaped and had finger-like sarcocyst wall protrusions, respectively. Under TEM, protrusions of S. frondea were about 9 × 1-1.5 μm, filled with clearly visible electron-dense substance and microtubules, type 39-like. Whereas, protrusions (about 9 × 0.2 μm) of S. nipponi arose from dome-shaped bases were filled with microtubules extending to the ground substance layer, type 9o-like. Moreover, three known Sarcocystis spp., Sarcocystis entzerothi, Sarcocystis ovalis, and Sarcocystis truncata previously described in other cervids as intermediate hosts, were characterized in sika deer. The cox1 was more suitable than 18S rDNA delimitating closely related Sarcocystis species from cervids. The phylogenetic results suggest that scavenger birds could be definitive hosts of S. frondea. According to the summarized morphological data on Sarcocystis found in the sika deer, such host should harbor at least nine different Sarcocystis species.

Caprine herpesvirus 2-associated malignant catarrhal fever of captive sika deer (Cervus nippon) in an intensive management system

Background

Caprine herpesvirus 2 (CpHV-2) infection usually induces chronic malignant catarrhal fever (MCF) in sika deer (Cervus nippon), with the primary signs of weight loss, dermatitis and alopecia.

Case presentation

Here, we report a case of CpHV-2-associated acute MCF in a sika deer herd raised in an intensive management system distant to the reservoir goats. Affected deer developed clinical signs of high fever (41 °C) followed by nasal discharge and lameness. Severe lesions of hemorrhage, necrosis and infiltration of lymphoid cells could readily be observed in the lung, kidney, heart valves and subcutaneous tissue surrounding a tendon. Etiologically, identical CpHV-2 specific DNA sequences were detected in peripheral blood lymphocyte (PBL) from the affected deer and reservoir goats.

Conclusion

In summary, domestic goats were the reservoir of the CpHV-2, which is the causative agent of the outbreak of MCF in the three hinds. The disease was probably transmitted via aerosol infection. In addition, necrosis and inflammation in subcutaneous tissue surrounding a tendon was the reason for lameness. Therefore, MCF should be put into a differential diagnostic list when similar disease occurs in sika deer herds.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1365-8) contains supplementary material, which is available to authorized users.

Genome-wide analysis of DNA methylation in five tissues of sika deer (Cervus nippon)

DNA methylation plays an important role in regulating gene expression during tissue development and differentiation in eukaryotes. In contrast to domestic animals, epigenetic studies have been seldom conducted in wild animals. In the present study, we conducted the genome-wide profiling of DNA methylation for five tissues of sika deer using the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique. Overall, a total of 104,131 fragments were amplified including 41,951 methylated fragments using 32 pairs of selected primers. The average incidence of DNA methylation was approximately 38.18% in muscle, 40.32% in heart, 41.86% in liver, 41.20% in lung, and 41.68% in kidney, respectively. Also, the significant differences of the DNA methylation levels were found between the different tissue types (P<0.05), which indicates that the differences of genome-wide DNA methylation levels may be related to gene expression during tissue development and differentiation. In addition, 37 tissue-specific differentially methylated regions (T-DMRs) were identified and recovered by MSAP in five tissues, and were further confirmed by Southern blot analysis. Our study presents the first look at the T-DMRs in sika deer and represents an initial step towards understanding of epigenetic regulatory mechanism underlying tissue development and differentiation in sika deer.

Isolation of novel microsatellite markers and their application for genetic diversity and parentage analyses in sika deer

Every part of the sika deer (Cervus nippon) body is valuable traditional Chinese medicine. And sika deer is the most important semi-domestic medicinal animal that is widely bred in Jilin province northeast of China. But few studies had been conducted to characterize the microsatellite markers derived from sika deer. We firstly used IlluminaHiSeq™2500 sequencing technology obtained 125Mbp genomic data of sika deer. Using microsatellite identification tool (MISA), 22,479 microsatellites were identified. From these data, 100 potential primers were selected for further polymorphic validation, finally, 76 primer pairs were successfully amplified and 29 primer pairs were found to be obvious polymorphic in 8 different individuals. Using those polymorphic microsatellite markers, we analyzed the genetic diversity of Jilin sika deer population. The mean number of alleles of the 29 loci is 9.31 based on genotyping blood DNA from 96 Jilin sika deer; The mean expected heterozygosity and polymorphic information content (PIC) value of the 29 loci is 0.72 and 0.68 respectively, and among which 26 loci are highly polymorphic (PIC>0.50). According to the electrophoretic results and PIC value of these 29 loci, 10 loci with combined paternity exclusion probabilities>99.99% were selected to use in parentage verification for 16 sika deer. All the offspring of a family could be successfully assigned to their biological father. These microsatellite markers generated in this study could greatly facilitate future studies of molecular breeding in sika deer.

Molecular identification and characterization of piroplasm species in Hokkaido sika deer (Cervus nippon yesoensis), Japan

Babesia and Theileria species are tick-borne protozoan parasites that have a veterinary and zoonotic importance. In order to investigate the prevalence and genetic diversity of these parasites, a total of 269 sika deer blood DNA samples collected from Hokkaido, Japan, were examined for Babesia and Theileria species by touch-down PCR targeting the 18S rRNA gene. Reverse line blot (RLB) hybridization was then used to detect 12 piroplasm species. The results revealed that 95.5% (257/269), 94.1% (253/269), 14.1% (38/269), 87.7% (236/269) and 11.5% (31/269) of the examined PCR products hybridized with the probes which were designed to detect all Babesia and Theileria spp., all Theileria spp., all Babesia spp., Theileria sp. Thrivae and Babesia divergens-like, respectively. The 18S rRNA gene partial sequences were divided into Theileria sp. Thrivae, T. capreoli, B. divergens-like and an undescribed Babesia species. This study showed the first detection of the undescribed Babesia sp. from Japan. Therefore, more studies are required to understand the ecology of the newly detected tick-borne pathogens in Hokkaido.

Molecular characterization of Fasciola flukes obtained from wild sika deer and domestic cattle in Hokkaido, Japan

The number of wild sika deer (Cervus nippon yesoensis) continues to increase in Hokkaido Prefecture, Japan. The major concern for the livestock industry is the transmission of pathogens between sika deer and cattle. Fasciolosis is an important disease that can occur in both animals. The aim of this study was to examine the possible mutual transmission of this disease in Hokkaido Prefecture. A total of 105 Fasciola flukes were obtained from sika deer and 96 from domestic cattle. The Fasciola flukes in Japan are reported to possess no mature sperm. However, in this study, 14 flukes from sika deer and eight flukes from cattle contained mature sperm in their seminal vesicles. All the Fasciola flukes from the two host animals had Fh/Fg type in nuclear phosphoenolpyruvate carboxykinase (pepck) gene, with a mixed fragment pattern derived from F. hepatica and F. gigantica, which are considered to be hybrid Fasciola flukes. However, almost all the flukes had Fsp1 haplotype in NADH dehydrogenase subunit 1 (nad1) gene, indicating that their maternal lineage was F. hepatica. A new haplotype, Fsp3, was detected in one fluke obtained from cattle and differed in one nucleotide from Fsp1. Therefore, the Fasciola flukes detected in both host species had almost identical molecular characteristics. These findings suggest the mutual transmission of Fasciola flukes between sika deer and domestic cattle in Hokkaido.

Identification and molecular survey of Borrelia burgdorferi sensu lato in sika deer (Cervus nippon) from Jilin Province, north-eastern China

Lyme disease caused by Borrelia burgdorferi sensu lato (s.l.) is a common disease of domestic animals and wildlife worldwide. Sika deer is first-grade state-protected wildlife animals in China and have economic consequences for humans. It is reported that sika deer may serve as an important reservoir host for several species of B. burgdorferi s.l. and may transmit these species to humans and animals. However, little is known about the presence of Borrelia pathogens in sika deer in China. In this study, the existence and prevalence of Borrelia sp. in sika deer from four regions of Jilin Province in China was assessed. Seventy-one blood samples of sika deer were collected and tested by nested-PCRs based on 16S ribosomal RNA (16S rRNA), outer surface protein A (OspA), flagenllin (fla), and 5S-23S rRNA intergenic spacer (5S-23S rRNA) genes of B. burgdorferi s.l. Six (8.45%) samples were positive for Borrelia sp. based on sequences of 4 genes. The positive samples were detected 18 for 16S rRNA, 10 for OspA, 16 for fla and 6 for 5S-23S, with the positive rates 25.35% (95% CI=3.8-35.6), 14.08% (95% CI=3.0-21.6), 22.54% (95% CI=4.3-36.9) and 8.45% (95% CI=1.7-22.9), respectively. Sequence analysis of the positive PCR products revealed that the partial 4 genes sequences in this study were all most similar to the sequences of B. garinii and B. burgdorferi sensu stricto (s.s.), no other Borrelia genospecies were found. This is the first report of Borrelia pathogens in sika deer in China. The findings in this study indicated that sika deer as potential natural host and may spread Lyme disease pathogen to animals, ticks, and even humans.

Transcriptome analysis of sika deer in China

Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development.

from the sika deer (Cervus nippon) in Lithuania

The diaphragm muscles of eight sika deer (Cervus nippon) bred in Lithuania were examined for Sarcocystis cysts. Two Sarcocystis species, Sarcocystis taeniata, which were previously reported in Canadian moose (Alces alces) and Argentinean red deer (Cervus elaphus), and Sarcocystis pilosa n. sp. were described using light microscopy (LM), transmission electron microscopy (TEM), 18S ribosomal DNA (rDNA), and subunit I of cytochrome c oxidase (cox1) sequences analysis. By LM, cysts of S. taeniata were 424.8 × 57.9 (200-837 × 30-100) μm in size and had a thin (up to 1 μm) and smooth cyst wall, while short ribbon-like protrusions arising from broadened cone-shaped bases were seen under TEM. Cysts of S. pilosa (by LM) were ribbon-shaped, measured 848.5 × 63.8 (350-1700 × 30-125) μm and had thin 7-8-μm long hair-like protrusions. By TEM, cyst wall was type 7a-like; protrusions arose from 0.3 μm wide dome-shaped base with minute indentations of the parasitophorous vacuolar membrane near it, the surface of protrusions seemed to be smooth, and the ground substance layer was thin (0.18-0.22 μm). The 18S rDNA, in contrast to the cox1, lacked variability to discriminate S. pilosa from closely related Sarcocystis hjorti from the red deer and moose. S. taeniata, but not S. pilosa, showed a considerable intraspecific variation in both genes analyzed. The phylogenetic analyses based on 18S rDNA and cox1 sequences suggest that canids are definitive hosts of both S. taeniata and S. pilosa. This paper represents the first identification of Sarcocystis species in the sika deer by morphological and molecular methods.

Molecular detection and identification of piroplasms in sika deer (Cervus nippon) from Jilin Province, China

Background

Piroplasmosis is an important disease of domestic animals and wildlife and is caused by organisms from the genera Theileria and Babesia. Wildlife such as sika deer play an important role as reservoir hosts for several species of Theileria and Babesia. Using blood samples collected from sika deer, we investigated the epidemiology of Theileria spp. and Babesia spp. in sika deer from Jilin Province in China and identified those species that cause pathogenic infections in sika deer.

Methods

Sixty-eight blood samples of sika deer were collected from three areas of the Jilin Province in Northeast China. Genomic DNA was extracted, and the V4 hypervariable region of the 18S rRNA of the piroplasms was amplified using the nested PCR method. The selected positive samples were sequenced to identify species of Babesia and Theileria.

Results

PCR detection revealed that 24 samples were positive for Theileria and Babesia spp. (35.29 %, 95 % CI = 11.8-46.8). After alignment, a sequenced fragment for Theileria cervi was found to be the most prevalent from the obtained samples (22.06 %, 95 % CI = 11.8-49.6). Six sika deer samples were identified as being infected with a Theileria sp. that was similar to a Theileria sp. found from spotted deer in India. In addition to the results above, for the first time, we identified T. annulata infection from one sample of sika deer and Babesia sp. from two samples, which showed high identity with Babesia motasi found in sheep from China.

Conclusion

The present study offers new data on the pathogens of piroplasmosis in sika deer in northeastern China. For the first time, sika deer was confirmed as a reservoir host for the T. annulata of cattle and the B. motasi of sheep, which was found in China.

Molecular detection and genetic characterization of Toxoplasma gondii infection in sika deer (Cervus nippon) in China

The objective of the present study was to investigate the prevalence and genetic characterization of Toxoplasma gondii infection in sika deer in China. During August 2014 to November 2014, a total of 450 tissue samples coming from 150 sika deer were collected to detect the T. gondii B1 gene using a nested PCR, and the positive samples were genotyped at 11 genetic markers (SAG1, 5'- and 3'-SAG2, alternative SAG2, SAG3, BTUB, GRA6, L358, PK1, c22-8, c29-2, and Apico) using multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. Seventeen of 150 sika deer (11.33%) were tested positive by nested PCR. Six DNA samples from the 17 positive samples were completely typed, in which 4 samples from lung tissues, and 2 from muscular tissues, were identified as ToxoDB Genotype #9 (http://toxodb.org/toxo/). The results of the present study revealed the existence of T. gondii infection in sika deer in China, which provided the information of T. gondii genetic diversity in this host species. This study also indicated that ToxoDB Genotype #9 has a wide distribution in sika deer that could be potential reservoirs for T. gondii transmission, which may pose a threat to human health.

The complete mitochondrial genome of Sika deer Cervus nippon hortulorum (Artiodactyla: Cervidae) and phylogenetic studies

Sika deer (Cervus nippon Temminck 1836) are classified in the order Artiodactyla, family Cervidae, subfamily Cervinae. At present, the phylogenetic studies of C. nippon are problematic. In this study, we first determined and described the complete mitochondrial sequence of the wild C. nippon hortulorum. The complete mitogenome sequence is 16 566 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition was 33.4% A, 28.6% T, 24.5% C, 13.5% G, with a 62.0% AT bias. The 13 protein-coding genes encode 3782 amino acids in total. To further validate the new determined sequences and phylogeny of Sika deer, phylogenetic trees involving 15 most closely related species available in GenBank database were constructed. These results are expected to provide useful molecular data for deer species identification and further phylogenetic studies of Artiodactyla.

Seroprevalence and risk factors of Toxoplasma gondii infection in domestic sika deer (Cervus nippon) in northeastern China

Toxoplasmosis is a worldwide zoonosis caused by Toxoplasma gondii, which can infect warm-blooded animals and humans. A serological survey was undertaken to examine the seroprevalence and risk factors associated with T. gondii infection in sika deer in northeastern China. 114 (13.46%, 95% CI 11.16-15.76) out of 847 serum samples were positive to T. gondii by modified agglutination test (MAT) at a 1:25 cut-off, with titers of 1:25 in 44, 1:50 in 32, 1:100 in 17, 1:500 in 11, 1:1500 or higher in 10. These samples were collected between November 2012 and October 2013 from Inner Mongolia, Jilin and Heilongjiang provinces in China. However, statistically significant differences were not observed between T. gondii seroprevalence and genders or regions of sika deer in the logistic regression analysis (P>0.05) and left out of the final model. Seroprevalence of T. gondii infection in male sika deer was 14.07% (95% CI 11.14-17.01), slightly higher than that in the female (12.38%) (95% CI 8.69-16.06) and seroprevalence of T. gondii infection in Harbin, Changchun city, Jilin city and Chifeng city were 12.02% (95% CI 7.60-16.44), 15.51% (95% CI 11.52-19.50), 12.27% (95% CI 7.23-17.31) and 12.50% (95% CI 7.38-17.63), respectively. Seasons of sampling were considered as main risk factors associated with T. gondii infection, autumn (15.32%) were more than two times (OR=1.98, 95% CI=1.18-3.33, P=0.01) at risk of acquiring T. gondii infection compared to winter (8.37%). Our results indicated a widespread exposure to T. gondii among sika deer in China. To our knowledge, this is the first report of T. gondii seroprevalence in sika deer in China.

ticks in Hokkaido, Japan

A relapsing fever Borrelia sp. similar to Borrelia lonestari (herein referred to as B. lonestari-like) was detected from wild sika deer (Cervus nippon yesoensis) and Haemaphysalis ticks in the eastern part of Hokkaido, Japan. The total prevalence of this Borrelia sp. in tested deer blood samples was 10.6% using conventional PCR and real-time PCR. The prevalence was significantly higher in deer fawns compared to adults (21.9% and 9.4%, respectively). Additionally, there was significant regional difference between our two sampling areas, Shiretoko and Shibetsu with 17% and 2.8% prevalence, respectively. Regional differences were also found in tick species collected from field and on deer. In the Shiretoko region, Haemaphysalis spp. were more abundant than Ixodes spp., while in Shibetsu, Ixodes spp. were more abundant. Using real-time PCR analysis, B. lonestari-like was detected from 2 out of 290 adult Haemaphysalis spp. ticks and 4 out of 76 pools of nymphs. This is the first report of a B. lonestari-like organism in Haemaphysalis spp. ticks, and the first phylogenetic analysis of this B. lonestari-like organism in Asia. Based on our results, Haemaphysalis spp. are the most likely candidates to act as a vector for B. lonestari-like; furthermore, regional variation of B. lonestari-like prevalence in sika deer may be dependent on the population distribution of these ticks.

Disturbance by large herbivores alters the relative importance of the ecological processes that influence the assembly pattern in heterogeneous meta-communities

Disturbance caused by large herbivores can affect the relative importance of ecological processes in determining community assembly and may cause a systematic loss of biodiversity across scales. To examine changes in the community assembly pattern caused by an overabundance of large herbivores in Japan, we analyzed community composition data from before and after the overabundance occurred. The community assembly pattern becomes more random after the deer overabundance. In addition, result of variation partitioning revealed decrease in importance of environmental processes and increase in importance of spatial processes. However, response of turnover rate, niche breadth, and niche overlap was heterogeneous, according to scale of each environmental gradient. Our results emphasize the importance of conserving habitat specialists that represent the local environment (habitat type and topography) at various altitudinal ranges to maintain biodiversity at regional scales under the increasing pressure of large herbivores.