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Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection.

Sevane N, Cañon J, Gil I, Dunner S - PLoS ONE (2015)

Bottom Line: Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR.Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis.This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.

ABSTRACT
Present and future challenges for wild partridge populations include the resistance against possible disease transmission after restocking with captive-reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios. Selection of individuals with the best immune ability may be a good strategy to improve general immunity, and hence adaptation to stress. In this study, non-infectious challenges with phytohemagglutinin (PHA) and sheep red blood cells allowed the classification of red-legged partridges (Alectoris rufa) according to their overall immune responses (IR). Skin from the area of injection of PHA and spleen, both from animals showing extreme high and low IR, were selected to investigate the transcriptional profiles underlying the different ability to cope with pathogens and external aggressions. RNA-seq yielded 97 million raw reads from eight sequencing libraries and approximately 84% of the processed reads were mapped to the reference chicken genome. Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis. These findings indicate that the immune system ability to respond to aggressions (either diseases or stress produced by environmental changes) involves extensive transcriptional and post-transcriptional regulations, and expand our understanding on the molecular mechanisms of the avian immune system, opening the possibility of improving disease resistance or robustness using genome assisted selection (GAS) approaches for increased IR in partridges by using genes such as AVN or BF2 as markers. This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.

No MeSH data available.


Related in: MedlinePlus

Functional analysis of differentially expressed genes between partridges with high and low IR.DAVID Functional Annotation Cluster (FAC) analysis was conducted on two independent gene lists containing 509 up-regulated genes and 40 down-regulated genes (0 ≤ q ≤ 0.5) under high stringency ease scores. In black: grouped FACs for up-regulated genes. In grey: grouped FACs for down-regulated genes.
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pone.0136776.g003: Functional analysis of differentially expressed genes between partridges with high and low IR.DAVID Functional Annotation Cluster (FAC) analysis was conducted on two independent gene lists containing 509 up-regulated genes and 40 down-regulated genes (0 ≤ q ≤ 0.5) under high stringency ease scores. In black: grouped FACs for up-regulated genes. In grey: grouped FACs for down-regulated genes.

Mentions: To obtain a comprehensive picture of the pathways and biological processes switched on/off as the IR grows stronger, the expression data was analysed using the DAVID tool. Among the 1,410 and 78 up-regulated sequences in skin and spleen samples respectively, 585 shared significant homology with chicken genes encoding proteins of known function (S3 Table). However, 3 of them matched two or more genes and were not considered for downstream analysis. Finally, DAVID FAC analysis included 509 up-regulated sequences in 187 clusters in the up-regulated group mainly for cellular proliferation, cell death, wound healing, immune response, and lytic activity processes (Fig 3, S4 Table). Among the 88 and 19 sequences down-regulated in skin and spleen samples, respectively, 47 shared significant homology with different chicken genes encoding proteins of known function (S3 Table). DAVID FAC analysis included 40 down-regulated sequences in the analysis and retrieved 19 clusters with lower enrichment scores (Fig 3, S4 Table).


Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection.

Sevane N, Cañon J, Gil I, Dunner S - PLoS ONE (2015)

Functional analysis of differentially expressed genes between partridges with high and low IR.DAVID Functional Annotation Cluster (FAC) analysis was conducted on two independent gene lists containing 509 up-regulated genes and 40 down-regulated genes (0 ≤ q ≤ 0.5) under high stringency ease scores. In black: grouped FACs for up-regulated genes. In grey: grouped FACs for down-regulated genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4557936&req=5

pone.0136776.g003: Functional analysis of differentially expressed genes between partridges with high and low IR.DAVID Functional Annotation Cluster (FAC) analysis was conducted on two independent gene lists containing 509 up-regulated genes and 40 down-regulated genes (0 ≤ q ≤ 0.5) under high stringency ease scores. In black: grouped FACs for up-regulated genes. In grey: grouped FACs for down-regulated genes.
Mentions: To obtain a comprehensive picture of the pathways and biological processes switched on/off as the IR grows stronger, the expression data was analysed using the DAVID tool. Among the 1,410 and 78 up-regulated sequences in skin and spleen samples respectively, 585 shared significant homology with chicken genes encoding proteins of known function (S3 Table). However, 3 of them matched two or more genes and were not considered for downstream analysis. Finally, DAVID FAC analysis included 509 up-regulated sequences in 187 clusters in the up-regulated group mainly for cellular proliferation, cell death, wound healing, immune response, and lytic activity processes (Fig 3, S4 Table). Among the 88 and 19 sequences down-regulated in skin and spleen samples, respectively, 47 shared significant homology with different chicken genes encoding proteins of known function (S3 Table). DAVID FAC analysis included 40 down-regulated sequences in the analysis and retrieved 19 clusters with lower enrichment scores (Fig 3, S4 Table).

Bottom Line: Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR.Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis.This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.

ABSTRACT
Present and future challenges for wild partridge populations include the resistance against possible disease transmission after restocking with captive-reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios. Selection of individuals with the best immune ability may be a good strategy to improve general immunity, and hence adaptation to stress. In this study, non-infectious challenges with phytohemagglutinin (PHA) and sheep red blood cells allowed the classification of red-legged partridges (Alectoris rufa) according to their overall immune responses (IR). Skin from the area of injection of PHA and spleen, both from animals showing extreme high and low IR, were selected to investigate the transcriptional profiles underlying the different ability to cope with pathogens and external aggressions. RNA-seq yielded 97 million raw reads from eight sequencing libraries and approximately 84% of the processed reads were mapped to the reference chicken genome. Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis. These findings indicate that the immune system ability to respond to aggressions (either diseases or stress produced by environmental changes) involves extensive transcriptional and post-transcriptional regulations, and expand our understanding on the molecular mechanisms of the avian immune system, opening the possibility of improving disease resistance or robustness using genome assisted selection (GAS) approaches for increased IR in partridges by using genes such as AVN or BF2 as markers. This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.

No MeSH data available.


Related in: MedlinePlus