A highly contiguous genome for the Golden-fronted Woodpecker (Melanerpes aurifrons) via a hybrid Oxford Nanopore and short read assembly

Abstract

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Woodpeckers are found in nearly every part of the world, absent only from Antarctica, Australasia, and Madagascar. Woodpeckers have been important for studies of biogeography, phylogeography, and macroecology. Woodpeckers hybrid zones are often studied to understand the dynamics of introgression between bird species. Notably, woodpeckers are gaining attention for their enriched levels of transposable elements (TEs) relative to most other birds. This enrichment of TEs may have substantial effects on woodpecker molecular evolution. The Golden-fronted Woodpecker (<jats:italic>Melanerpes aurifrons</jats:italic>) is a member of the largest radiation of New World woodpeckers. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>Using hybrid assembly methods that combine long-read Oxford Nanopore and short-read Illumina sequencing data, we generated a highly contiguous genome assembly for the Golden-fronted Woodpecker. The final assembly is 1.31 Gb and comprises 441 contigs plus a full mitochondrial genome. Half of the assembly is represented by 28 contigs (contig N50), each of these contigs is at least 16 Mb in size (contig L50). High recovery (92.6%) of bird-specific BUSCO genes suggests our assembly is both relatively complete and relatively accurate. Accuracy is also demonstrated by the recovery of a putatively error-free mitochondrial genome. Over a quarter (25.8%) of the genome consists of repetitive elements, with 287 Mb (21.9%) of those elements assignable to the CR1 superfamily of transposable elements, the highest proportion of CR1 repeats reported for any bird genome to date.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Our assembly provides a useful tool for comparative studies of molecular evolution and genomics in woodpeckers and allies, a group emerging as important for studies on the role that TEs may play in avian evolution. Additionally, the sequencing and bioinformatic resources used to generate this assembly were relatively low-cost and should provide a direction for the development of high-quality genomes for future studies of animal biodiversity.</jats:p></jats:sec>

De Novo Assembly of a Chromosome-Scale Reference Genome for the Northern FlickerColaptes auratus

“…While a higher gene group recovery rate would be expected for a highly-contiguous assembly, we highlight that these results correspond with studies that have found that greater assembly contiguity often does not result in an increased gene group recovery rate, and if an increase is noted, it is often modest (Korlach et al 2017;Low et al 2019). Indeed, we find our recovery rates to be similar to those of the Melanerpes aurifrons assembly, with 92.6 % of complete BUSCO gene groups recovered from the aves_odb9 dataset (Wiley and Miller 2020). We recovered a high degree of one-to-one synteny with the Chicken Gallus gallus chromosomes, particularly between those of small and medium size ( Figure 1B).…”

Population genomics of an emergent tri‐species hybrid zone

“…Our assembly is 96% complete with 88% complete single copy BUSCOs, 8% complete duplicated, 0.9% fragmented, and 3.1% missing. Finally, we used the Chromosemble tool in satsuma version 2.0 (Grabherr et al, 2010) to align our contigs to a Golden‐fronted Woodpecker ( Melanerpes aurifrons ) genome (Wiley & Miller, 2020). Our final assembled genome had 269 scaffolds.…”

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…Complex genomes often result in highly fragmented assemblies (Koren et al, 2012; Rice & Green, 2019). The development of less accurate but long-read sequencing technologies from Oxford Nanopore and Pacific Biosciences (PacBio) has improved the assembly process by combining them with short-read data to create “hybrid”, more contiguous genome assemblies (Austin et al, 2017; Dhar et al, 2019; Jiang et al, 2019; Tan et al, 2018; Wiley & Miller, 2020; Zimin, Puiu, et al, 2017; Zimin, Stevens, et al, 2017).…”