Molecular tools to support metabolic and immune function research in the Guinea Fowl (Numida meleagris)

Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Whole transcriptome-based miRNA-mRNA network analysis revealed the mechanism of inflammation-immunosuppressive damage caused by cadmium in common carp spleens

Cadmium (Cd) is a well-known environmental pollutant and can damage fish. MicroRNAs (miRNAs) can involve in inflammation and immunosuppression. However, the mechanisms of miRNAs are still unclear in common carp (Cyprinus carpio L.) treated by Cd. In current study, 54 juvenile common carp were randomly divided into the control group and the Cd group (0.26 mg L^-1 Cd) and were cultured for 30 days. The results revealed inflammatory damage in the spleens of common carp after Cd exposure using morphological construction. There were 23 differentially expressed miRNAs including 17 up-regulated differentially expressed miRNAs (miR-1-4-3p, miR-7-1-5p, miR-7-2-5p, miR-10-43-5p, miR-34-3-5p, miR-128-4-3p, miR-128-5-3p, miR-132-2-5p, miR-132-6-5p, miR-216-3-5p, miR-216-4-5p, miR-375-2-3p, miR-375-4-3p, miR-375-5-3p, miR-375-7-3p, miR-375-8-3p, and miR-724-5p) and 6 down-regulated differentially expressed miRNAs (miR-9-6-5p, miR-25-9-3p, miR-31-3-5p, miR-31-12-5p, miR-103-5-5p, and miR-122-1-3p). The 23 miRNAs regulated 2022 target mRNAs. There were 10 pathways and 9 annotation clusters on 2022 target mRNAs using KEGG and GO analysis, respectively. Among them, 5 pathways (NF-κB signaling pathway, Jak-STAT signaling pathway, MAPK signaling pathway, Th1 and Th2 cell differentiation, and Toll-like receptor signaling pathway) and 7 GO terms (negative regulation of immune system process, T cell mediated immunity, regulation of immune response, inflammatory response, positive regulation of inflammatory response, regulation of inflammatory response, and inflammasome complex) were associated with inflammatory response and immunosuppression. miR-375-4-3p, NF-κB, COX-2, PTGES, and IL-4/13A increased and miR-31-12-5p, miR-9-6-5p, MMP9, IL-11, SPI1, and T-Bet decreased using transcriptome sequencing and RT-qPCR in Cd-treated common carp spleens, which revealed that our results were reliable. Our data indicated that miRNAs mediated inflammation-immunosuppressive injury caused by Cd in common carp spleens using whole transcriptome-based miRNA-mRNA network analysis. Our study provided new insights into the toxicology of Cd exposure.