Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

Ros‐Freixedes, Roger; Pena, Ramona N.; Richart, C.; Nadal, Jesús

doi:10.1016/j.ygeno.2023.110591

Cited by 3 publications

(6 citation statements)

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“…At the same time, the greater high variant density and the large number of rare variants that arise from whole-genome sequencing hinder the detection of ROH when using a reference genome from a different species (see F ROH in Table 3 ). Nonetheless, all inbreeding coefficients with all tested reference genomes support greater inbreeding for the farm-reared population than for the wild population, which is more consistent with expectations for captive-bred populations than our previous estimates using the quail reference genome 14 .…”

Section: Technical Validationsupporting

confidence: 85%

“…The short-insert paired-end libraries for the whole-genome sequencing were prepared with a PCR-free protocol using KAPA HyperPrep kit as detailed before 14 . The 60 libraries were sequenced on NovaSeq6000 (Illumina) in paired-end mode with a read length of 2x151+17+8 bp following the manufacturer’s protocol for dual indexing.…”

Section: Methodsmentioning

confidence: 99%

“…In a previous study we used the reference genome of the quail to align the whole-genome sequence data of wild and farm-reared red-legged partridges to study their genetic variation, inbreeding, population structure and selective sweeps 14 . We benchmarked our new Arufa2 reference genome by comparing to Arufa1 and the quail reference genome.…”

Section: Methodsmentioning

confidence: 99%

“…Muscle samples for whole-genome sequencing were collected from 60 red-legged partridges, divided in two subpopulations. Half of the samples (n=30) were from a population of wild partridges from a private game hunting state in central Spain ("Las Ensanchas", Ciudad Real, Spain) and the other half (n=30) were from a partridge rearing farm (more information in Ros-Freixedes et al 14 ). These 60 samples were sequenced in an Illumina (San Diego, CA, USA) short-read platform, as described below.…”

Section: Sample Collection and Construction Of Sequencing Librariesmentioning

confidence: 99%

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Long-readde novoassembly of the red-legged partridge (Alectoris rufa) genome

González-Prendes,

Pena,

Richart

et al. 2024

Preprint

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The red-legged partridge (Alectoris rufa) is a popular game bird species that is in decline in several regions of southwestern Europe. The introduction of farm-reared individuals of a distinct genetic make-up in hunting reserves can result in genetic swamping of wild populations. Here we present a de novo genome assembly for the red-legged partridge based on long-read sequencing technology. The assembled genome size is 1.14 Gb, with scaffold N50 of 37.6 Mb and contig N50 of 29.5 Mb. Our genome is highly contiguous and contains 97.06% of complete avian core genes. Overall, quality of this genome assembly is equivalent to those available for other close relatives such as the Japanese quail or the chicken. This genome assembly will contribute to the understanding of genetic dynamics of wild populations of red-legged partridges with releases of farm-reared reinforcements and to appropriate management decisions of such populations.

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Section: Technical Validationsupporting

confidence: 85%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Sample Collection and Construction Of Sequencing Librariesmentioning

confidence: 99%

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Long-readde novoassembly of the red-legged partridge (Alectoris rufa) genome

González-Prendes,

Pena,

Richart

et al. 2024

Preprint

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“…Across various hunting grounds, wild, farmed, and hybrid partridges coexist in varying proportions. While these partridges exhibit distinctions in behavior, physiology, morphology, anatomy, and genetics, the absence of a reference genome hinders our ability to molecularly differentiate these ecotypes, spanning from wild to domestic 2 . The haploid genome of A. rufa has 10 macro chromosomes, two of which are sex chromosomes, and 30 micro chromosomes 3,4 .…”

Section: Introductionmentioning

confidence: 99%

An almost chromosome-level assembly and annotation of theAlectoris rufagenome

Eleiwa,

Nadal,

Vilaprinyo

et al. 2024

Preprint

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The red-legged partridge,Alectoris rufa(n=38 chromosomes) plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of it genome (115 scaffolds, L90=23). This assembly contains 96.9% (8078 out of 8332) orthologous genes from the BUSCO aves_odb10 dataset of single copy orthologous genes. We identify RNA and protein genes, 95% of which with functional annotation. This near-chromosome level assembly revealed significant chromosome rearrangements compared to quail (Coturnix japonica) and chicken (Gallus gallus), suggesting thatA. rufaandC. japonicadiverged 21 M-years ago and that their common ancestor diverged fromG. gallus37 M-years ago. The reported assembly is a significant step towards a complete reference genome forA. rufa, contributing to facilitate comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.

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