Project description:The leaf muntjac (Muntiacus putaoensis) is an endemic deer species found in the east trans-Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses (ML and BI) among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.
Project description:Studies of the miRNA expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of miRNAs from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 171 known miRNAs and 60 novel miRNAs were identified based on four small RNA libraries. 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 4 miRNAs were differentially expressed between adult and adolescence sika deer, and 1 miRNAs were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that miRNA were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that miR-133a, miR-133c, miR-192, miR-151-3p etc. may play important roles in muscle growth and development, and miR-17-5p, miR-378b, miR-199a-5p, miR-7 etc. may have key roles in muscle aging. In this study, we determined the dynamic miRNA in muscle tissue for the first time in sika deer. The age-dependent miRNAs identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.
2020-01-11 | GSE142978 | GEO
Project description:Hi-C Sequencing unravels dynamic 3D chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome
Project description:To elucidate the complex physiological process of the growth, development and immunity response of Sika Deer, this study evaluated the changes of miRNA profiles in the four developmental stages (juvenile, adolescence, adult and aged) of ten tissue (adrenal, antler, brain, heart, kidney, lung, liver, skeletal muscle, spleen and testes). The results showed that a total of 306 known miRNAs and 143 novel miRNAs were obtained. Many miRNAs displayed organ-specificity and age-specificity. The largest number of miRNAs were enriched in the brain, some of which were shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. Additionally, the adolescence-adult transition of Sika Deer was a crucial stage in its life cycle. In conclusion, our study provided abundant data support for the current research Sika Deer. It also contributes to understand the role of miRNAs play in regulating the growth, development and immunity response of Sika Deer.
Project description:Muntjac deer (Cervidae: Muntiacus) are often cited as an excellent model for the study of vertebrate evolution due to their fast rate of change in chromosome number among vertebrates. However, the phylogenetic relationships within Muntiacus generally, and the taxonomic status of Muntiacus gongshanensis specifically, remain unclear. Here, the phylogenetic relationships within Muntiacus were studied using mitochondrial genome (mitogenome) and cytochrome b (cyt b) segments. Our results recognize 12 species within Muntiacus and support the controversial species M. gongshanensis, M. putaoensis, and M. malabaricus. Furthermore, Bayesian inference (BI) and maximum-likelihood (ML) approaches revealed M. gongshanensis and M. crinifrons to be closely related species, with M. feae as their sister species, and M. putaoensis and M. truongsonensis to be closely related, with M. rooseveltorum as their sister species. The distribution range of M. gongshanensis was also confirmed in southwest China (Namdapha, Modong, Zayu and Gongshan) and northern Myanmar (Putao). The results of this study provide insight into the evolution of Muntiacus and further provide a molecular basis for the taxonomic evaluation of the genus in the future and fundamental data for the conservation of M. gongshanensis.
Project description:Studies of the gene expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of unigenes from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 51716 unigenes were identified based on four mRNA libraries. 2044 unigenes were differentially expressed between adolescence and juvenile sika deer, 1946 unigenes were differentially expressed between adult and adolescence sika deer, and 2209 unigenes were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that DE unigenes were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that Myh1, Myh2, Myh7, ACTN3 etc. may play important roles in muscle growth and development, and WWP1, DEK, UCP3, FUS etc. may have key roles in muscle aging. In this study, we determined the dynamic unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.
Project description:Bovine tuberculosis (bTB), caused by Mycobacterium bovis (Mycobacterium tuberculosis complex), is a zoonotic disease that affects cattle and wildlife worldwide. In some regions of Spain, Iberian red deer (Cervus elaphus hispanicus) can serve as reservoir of infection, thus increasing the risk of human and cattle exposure and infection. Mesenteric lymph nodes are naturally infected with M. bovis in Iberian red deer, in which the digestive route of infection is particularly important in Mediterranean Spain. In this study we characterized the differential expression of inflammatory and immune response genes in mesenteric lymph nodes of Iberian red deer naturally infected with M. bovis using a Ruminant Immuno-inflammatory Gene Universal Array (RIGUA) and real-time RT-PCR. Of the 600 genes that were analyzed in the microarray, 157 showed ? 1.2 fold changes in expression in infected or uninfected deer and 17 genes displayed an expression fold change greater than 1.7 with a P-value ? 0.05 and were selected for further analysis. These genes included tight junction proteins (Z02 and occluding), IL-11R, bactenecin, CD62L, CD74, desmoglein, IgA and IgM that constitute new findings and suggest new mechanisms by which M. bovis may modulate host inflammatory and immune responses. Identification of genes differentially expressed in animals and tissues naturally infected with M. bovis contributes to our basic understanding of the mechanisms of pathogenesis and protective immunity to mycobacterial infections and may have important implications for future functional genomic and vaccine studies to aid in the control of bTB in deer and other wildlife reservoir species. Mesenteric lymph node RNA from four different uninfected Iberian red deer stags and two Iberian red deer stags infected with Mycobacterium bovis. Infected animals were naturally infected with M. bovis. All animals were hunter-harvested and the tissues retrieved 2-6 hrs after animal hunting.
Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.