A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly

Abstract

Woodpeckers are found in nearly every part of the world and have been important for studies of biogeography, phylogeography, and macroecology. Woodpecker 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 molecular evolution. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species. Using hybrid assembly methods combining long-read Oxford Nanopore and short-read Illumina sequencing data, we generated a highly contiguous genome assembly for the Golden-fronted Woodpecker (Melanerpes aurifrons). 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 L50), each of these contigs is at least 16 Mb in size (contig N50). High recovery (92.6%) of bird-specific BUSCO genes suggests our assembly is both relatively complete and relatively accurate. 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. Our assembly should improve comparative studies of molecular evolution and genomics in woodpeckers and allies. Additionally, the sequencing and bioinformatic resources used to generate this assembly were relatively low-cost and should provide a direction for development of high-quality genomes for studies of animal biodiversity.

De novoassembly 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 M. 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 ).…”

“…The final assembly had an L50 of 43.938 Mbp scaffolds and an N50 of 11 ( Figure 1A; Table 1 ). In terms of contiguity (L50 and N50), this assembly represents a ∼3× improvement over a recently published long-read-based Picidae assembly ( Melanerpes aurifrons GCA_011125475.1; Wiley and Miller 2020 ) and represents the first published chromosome-level assembly for Piciformes. BUSCO results also suggested this assembly is of high quality, with modestly high recovery of complete bird-specific and tetrapod-specific gene groups (87.4–91.7%; Table 2 ; Supplementary Files S1–S12).…”

“…Piciformes, on the other hand, are somewhat of an exception, and are well-known to contain some of the highest densities of TEs in birds ( Kapusta and Suh 2017 ), with repetitive densities often greater than 20% ( e.g. , Zhang et al 2014 ; Manthey et al 2018 ; Wiley and Miller 2020 ). The presence of the retrotransposon superfamily CR1 (chicken repeat 1) was particularly prevalent, comprising ∼20.9% (∼287 Mbp) of the Caur_TTU_1.0 assembly.…”

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 ). Combining short reads with less accurate long-read sequencing technologies leads to more contiguous genome assemblies ( Austin et al ., 2017 ; Zimin, Puiu, et al ., 2017 ; Zimin, Stevens, et al ., 2017 ; Tan et al ., 2018 ; Dhar et al ., 2019 ; Jiang et al ., 2019 ; Wiley & Miller, 2020 ). On the other hand, the relatively young circular consensus sequencing (CCS) PacBio technology produces reads that are both thousands of bp long and highly accurate.…”

MOSGA 2: Comparative genomics and validation tools

“…However, the generation of highquality eukaryotic genomes has been hampered in the past by sequencing costs and assembly complexity, limiting sequenced eukaryotes to those of medical or economical interest (7). More recently, advances in Illumina high-throughput sequencing and emerging long-read sequencing technologies developed by Pacific Biosciences and Oxford Nanopore have also rendered the generation of genome assemblies of large eukaryotes a routine task (8)(9)(10). These proceeding trends in data availability, advanced techniques, and improved affordability require more facilitated access for scientists to analyze these sequence data.…”