Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies. This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV. Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes “PPFGAGRPGQFGDI” showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides ‘TAECKDKNL’ and MHC class II peptides ‘VRYKCNCGG’ were found extremely antigenic. The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.

Gastrointestinal nematodes (GINs) are one of the most economically important parasites of small ruminants and a major animal health concern in many regions of the world. However, the molecular mechanisms of the host response to GIN infections in goat are still little known. In this study, two genetically distinct goat populations, one relatively resistant and the other susceptible to GIN infections, were identified in Yichang goat and then four individuals in each group were chosen to compare mRNA expression profiles using RNA-seq. Field experiment showed lower worm burden, delayed and reduced egg production in the relatively resistant group than the susceptible group. The analysis of RNA-seq showed that 2369 genes, 1407 of which were up-regulated and 962 down-regulated, were significantly (p < 0.001) differentially expressed between these two groups. Functional annotation of the 298 genes more highly expressed in the resistant group yielded a total of 46 significant (p < 0.05) functional annotation clusters including 31 genes (9 in innate immunity, 13 in immunity, and 9 in innate immune response) related to immune biosynthetic process as well as transforming growth factor (TGF)-β, mitogen-activated protein kinase (MAPK), and cell adhesion molecules (CAMs) pathways. Our findings provide insights that are immediately relevant for the improvement of host resistance to GIN infections and which will make it possible to know the mechanisms underlying the resistance of goats to GIN infections.

Background: The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results: Based on whole-genome resequencing data of 78 ducks ( Anas platyrhynchos ) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes ( PNPLA8 , THAP5 , and DNAJB9 ) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC ) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R ). Conclusions: Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

Somatic cloning has played important roles in animal production, basic science and human medical research. However, the epigenetic variation between cloned and donor animals is unclear, and low efficiency limits the application of somatic cloning. DNA methylation is a common epigenetic pattern in mammals and an important factor of phenotype in animals. To explore the cloning effect on the epigenetic inheritance and phenotype of cloned animals, we selected the blood and ear of one cloned pig and one donor pig to perform a whole-genome bisulphite sequencing to reveal the epigenetic modifications in cloning. A total of 216 and 707 differential methylation genes (DMGs) were identified in the blood and ear, respectively. The functional annotation showed that DMGs were enriched in many pathways, including T/B or NK cell differentiation, oocyte maturation, embryonic development and reproductive hormone secretion. Moreover, 22 and 75 DMGs in the blood and ear, respectively, were associated with immunity. The important immune regulatory factors, namely, CD244, CDK6, CD5, CD2, CD83 and CDC7, were differentially methylated between the cloned and donor pigs, possibly leading to immune differences of these two pigs. Meanwhile, 18 and 53 DMGs in the blood and ear, respectively, and the important genes, namely, ITPR2, TAPT1, GNAS and EGFR, were related to reproduction. Such genes were differentially methylated in the two pigs, possibly leading to low fertility of the cloned pig. Epigenetic variation existed between the cloned pig and the donor pig. Additionally, the genes related to immunity and reproduction differed in methylation between these two pigs, but they did not necessarily result in a significant phenotypic abnormality of cloned animals. However, the phenotypic variation caused by cloning had few effects on animal production, suggesting an effective way of achieving high-yielding animal production.