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

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.

An almost chromosome-level assembly and annotation of theAlectoris rufagenome

“…Our gene enrichment analysis suggests that A. rufa evolved a distinct set of regulatory genes and viral response proteins, likely shaped by species-specific infections and pressures. These findings align with previous transcriptomic analyses that highlighted heightened immune responses in the A. rufa 30 S6) highlight that the divergence between A. rufa and C. japonica is far from recent. For example, aligning scaffold 1 of A. rufa to chromosome 2 of C. japonica reveals an inversion that contains the centromeric region of the chromosome.…”

Eco‐immunology and bioinvasion: revisiting the evolution of increased competitive ability hypotheses

“…Few genome scan studies have yet been developed to examine the role that adaptive processes may play in the course of biological invasions (Quéméré et al, 2015;White et al, 2013). The use of transcriptomic approaches or high-throughput gene expression measures targeting immune genes could also be interesting, as they have successfully been done in a variety of eco-immunological studies, albeit not in an invasion context (Sevane, CaÒon, Gil, & Dunner, 2015).…”

Red-legged partridge ( Alectoris rufa ) de-novo transcriptome assembly and identification of gene-related markers

“…acquired IR) as well as a skin test with phytohemagglutinin (PHA) to quantify T cell-mediated IR (i.e. innate IR) (see [12] for details). A total of sixteen RNA samples from spleen ( n = 4), bursa of Fabricius ( n = 4), thymus ( n = 4) and the skin from PHA injection area ( n = 4) were extracted as detailed in Sevane et al [12] and pooled (300 ng each).…”

“…innate IR) (see [12] for details). A total of sixteen RNA samples from spleen ( n = 4), bursa of Fabricius ( n = 4), thymus ( n = 4) and the skin from PHA injection area ( n = 4) were extracted as detailed in Sevane et al [12] and pooled (300 ng each). These samples included two males and two females from each tissue, and the animals displaying the highest and the lowest IR.…”

“…Up to date, a solely differential expression analysis was performed in Sevane et al [12] on Gallus gallus given that the RNA-seq protocol used (single-end 75 bp) and the number of reads analysed (~ 12 million raw reads per sample) did not allow for transcriptome de-novo assembly. In this study, we analysed for the first time different tissues implicated in both innate and acquired immune response (IR) using a high coverage 100-bp paired-end RNA-seq protocol for the reliable identification of partridge genes and markers.…”