Dataset Information

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

ABSTRACT: The red-legged partridge (Alectoris rufa) has a great socio-economic importance as a game species and is reared by millions in farms in several European countries. The ability to respond to a wide spectrum of pathogens and environmental changes is key for farm-reared animals that, as such, face even higher pathogen exposure and specifically for those submitted to restocking programs. In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues were performed. The raw FASTQ files were submitted to the NCBI SRA database with accession number PRJNA289204. A total of 94.2 million reads were obtained and assembled into 51,403 contigs using OASES software. The final annotated partridge immune transcriptome comprises almost 7000 unigenes, available as FASTA in the supplementary material. A total of 12,828 microsatellites and 33,857 Single Nucleotide Polymorphisms (SNPs) were identified. The candidate gene sequences and the large number of potential genetic markers from the red-legged partridge transcriptome reliably identified through the use for the first time of a high coverage 100-bp paired-end RNA-seq protocol, provide new tools for future studies in this and related species, thus contributing to the ongoing development of genomic resources in avian species. Further investigation into candidate genes and gene-associated markers will help to uncover individual variability in the resistance to infections and other external aggressions in partridges.

SUBMITTER: Sevane N

PROVIDER: S-EPMC5304236 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Publications

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

Sevane Natalia N Cañon Javier J Eusebi Paulina G PG Gil Ignacio I Dunner Susana S

Genomics data 20170205

The red-legged partridge (Alectoris rufa) has a great socio-economic importance as a game species and is reared by millions in farms in several European countries. The ability to respond to a wide spectrum of pathogens and environmental changes is key for farm-reared animals that, as such, face even higher pathogen exposure and specifically for those submitted to restocking programs. In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues w ...[more]

PMID: 28239549

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Project description: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.

Project description:The reduction of game and fish populations has increased investment in management practices. Hunting and fishing managers use several tools to maximize harvest. Managers need to know the impact their management has on wild populations. This issue is especially important to improve management efficacy and biodiversity conservation. We used questionnaires and field bird surveys in 48 hunting estates to assess whether red-legged partridge Alectoris rufa young/adult ratio and summer abundance were related to the intensity of management (provision of supplementary food and water, predator control and releases of farm-bred partridges), harvest intensity or habitat in Central Spain. We hypothesized that partridge abundance would be higher where management practices were applied more intensively. Variation in young/adult ratio among estates was best explained by habitat, year and some management practices. Density of feeders and water points had a positive relationship with this ratio, while the density of partridges released and magpies controlled were negatively related to it. The variables with greatest relative importance were feeders, releases and year. Variations in post-breeding red-legged partridge abundance among estates were best explained by habitat, year, the same management variables that influenced young/adult ratio, and harvest intensity. Harvest intensity was negatively related to partridge abundance. The other management variables had the same type of relationship with abundance as with young/adult ratio, except magpie control. Variables with greatest relative importance were habitat, feeders, water points, releases and harvest intensity. Our study suggests that management had an overall important effect on post-breeding partridge abundance. However, this effect varied among tools, as some had the desired effect (increase in partridge abundance), whereas others did not or even had a negative relationship (such as release of farm-reared birds) and can be thus considered inefficient or even detrimental. We advise reconsidering their use from both ecological and economical points of view.

Dataset Information

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

Publications

Red-legged partridge (<i>Alectoris rufa</i>) <i>de-novo</i> transcriptome assembly and identification of gene-related markers.

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