Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos)

Abstract

The mallard (Anas platyrhynchos) is one of the most common, economically, and socially important birds around the world. Mallards were not only an important food source for early humans, but eventually becoming intimately linked with people as they were domesticated over the last 2,000 years. To date, mallard genomes are largely reconstructed from samples of domestic or unknown genetic heritage. Here, we report the first high-quality genome assembly and annotation of a genetically vetted wild mallard from North America (NAwild_v1.0). The genome was assembled using a combination of shotgun libraries and proximity ligation ChicagoTM and Dovetail Hi-CTM libraries, respectively. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 79.1 Mb/4 scaffolds. We used a combination of gene prediction and similarity approaches to annotate a total of 23,584 functional genes, of which 19,242 were associated to GO terms. The genome assembly and the set of annotated genes yielded a 95.4% completeness score when compared with the BUSCO aves_odb10 dataset. Next, we aligned three previously published mallard genomes to ours, and demonstrate how runs of homozygosity and nucleotide diversity are substantially higher and lower, respectively, to ours and how these artificially changed genomes resulted in profoundly different and biased demographic histories. Our wild mallard assembly not only provides a valuable resource to shed light onto genome evolution, speciation and other adaptive processes, but also helping with identifying functional genes that have been significantly altered during the domestication process.

Human-Induced Range Expansions Result in a Recent Hybrid Zone between Sister Species of Ducks

“…The domestic lineages included known game farm mallards and Khaki Campbells ( A. p. domesticus ), with the latter serving as a genetic signature of a “park” duck. All sequences were first trimmed or discarded for poor quality using Trimmomatic [ 29 ], and then remaining quality reads were aligned to a reference wild mallard genome [ 30 ] using the Burrows Wheeler Aligner v. 07.15 (bwa; [ 31 ]). Next, samples were sorted and indexed in SAMtools v. 1.6 [ 32 ] and combined using the “mpileup” function within bcftools (part of SAMtools v. 1.6) with the following parameters: “-c –A -Q 30 -q 30”.…”

Consistent changes in muscle metabolism underlie dive performance across multiple lineages of diving ducks

“…Using VCF tools v. 0.1.15 [ 36 ], we further filtered the sequences for missing data (greater than 20% of samples), minimum base-pair depth of coverage of 5× (10× per genotype) and per base PHRED quality scores of greater than or equal to 30. All sequences were aligned to a chromosomally assembled wild mallard ( Anas platyrhychos ) genome [ 37 ], which allowed us to distinguish between autosomal and sex-linked ddRAD-seq loci.…”