Numida meleagris
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA168045 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1210380.fastq.gz | Fastqsanger.gz | |||
| SRR1213063.fastq.gz | Fastqsanger.gz | |||
| SRR828636.fastq.gz | Fastqsanger.gz | |||
| SRR830283.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description:Numida Meleagris uterine Transcriptome
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Project description:Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000.74 million sequences were generated and assembled into 96,492 contigs using the Trinity software suite. Over 39,000 of these transcripts were found to have in silico translated protein sequences that are homologous to chicken protein sequences. Gene ontology analysis uncovered 416 transcripts with metabolic functions and 703 with immune function.The transcriptome information presented here will support the development of molecular approaches to improve production efficiency of the guinea fowl and other avian species.
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Project description:Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
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Project description:Crossover rates and localization are not homogeneous throughout the genomes. Along the chromosomes of almost all species, domains with high crossover rates alternate with domains where crossover rates are significantly lower than the genome-wide average. The distribution of crossovers along chromosomes constitutes the recombination landscape of a given species and can be analyzed at broadscale using immunostaining of the MLH1 protein, a component of mature recombination nodules found on synaptonemal complexes during pachytene. We scored the MLH1 foci in oocytes of the chicken and the guinea fowl and compared their frequencies in the largest bivalents. The average autosomal number of foci is 62 in the chicken and 44 in the guinea fowl. The lower number in the guinea fowl responds to the occurrence of fewer crossovers in the six largest bivalents, where most MLH1 foci occur within one-fifth of the chromosome length with high polarization towards opposite ends. The skewed distribution of foci in the guinea fowl contrast with the more uniform distribution of numerous foci in the chicken, especially in the four largest bivalents. The crossover distribution observed in the guinea fowl is unusual among Galloanserae and also differs from other, more distantly related birds. We discussed the current evidence showing that the shift towards crossover localization, as observed in the guinea fowl, was not a unique event but also occurred at different moments of bird evolution. A comparative analysis of genome-wide average recombination rates in birds shows variations within narrower limits compared to mammals and the absence of a phylogenetic trend.
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Project description:To understand the effectiveness of a probiotic mixture on intestinal morphology, mucus layer composition, and cecal microbiota diversity, 40 10-day-old Guinea fowls (Numida meleagris) were assigned to two groups: the control group (C), receiving drinking water, and the treated group (P), receiving water plus a commercial multi-strain probiotic (Slab51®, 2 × 1011 CFU/L). Birds were slaughtered after 4 months, and the intestines were collected. Samples from the duodenum, ileum, and cecum were processed for morphological and morphometric studies, and conventional glycohistochemistry. Cecal samples were also used to assess the microbiota by 16S metataxonomic approach. Group P showed significant increase in the villus height (p < 0.001 in the duodenum and p < 0.05 in the ileum and cecum), villus width (p < 0.05 in all investigated tracts), depth of crypts (p < 0.001 in the duodenum and cecum; p < 0.05 in the ileum), and goblet cells per villus (p < 0.001 in all investigated tracts) compared with group C. Cecal microbiota of the birds varied considerably and comparing the relative abundance of the main observational taxonomic units (OTUs), a positive enrichment of several beneficial taxa, such as Oscillospira, Eubacterium, Prevotella, and members of the Ruminococcaceae, was observed. The enrichment of those taxa can improve microbiota stability and resilience facing environmental stresses, enhancing its resistance against invading pathogens. Ruminococcaceae, which represent the most important taxon in both groups, and Prevotella have a key role in the gut physiology due to the production of short-chain fatty acids (SCFAs), which are a vital energy source for enterocytes, improve glucose metabolism, and exert an overall anti-inflammatory effect. Probiotic administration enriches the presence of Coprococcus, Oscillospira, and Eubacterium taxa that produce butyrate, which exerts a beneficial effect on growth performance, structure of villi, and pathogen control and has anti-inflammatory properties too. This study indicates that Slab51® supplementation positively affects the morphology and microbiota diversity of the guinea fowl intestine.
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