TY - JOUR
T1 - A highly contiguous genome for the golden-fronted woodpecker (Melanerpes aurifrons) via hybrid oxford nanopore and short read assembly
AU - Wiley, Graham
AU - Miller, Matthew J.
N1 - Funding Information:
Funding for this research was provided by the Sam Noble Oklahoma Museum of Natural History. We also received a subsidy through the University of Oklahoma Consolidated Core Lab for Illumina sequencing which was undertaken at the Oklahoma Medical Research Foundation (OMRF) Clinical Genomics Center. Promethion library preparation and sequencing was carried out by Ruta Sahasrabudhe at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01. We thank OMRF for providing access to their computation cluster for data analysis. Scientific collecting was authorized by the Texas Parks and Wildlife Department and the United States Fish and Wildlife Service and supported by the Ornithology Department at the Sam Noble Museum. We thank them for their support of scientific collecting. We thank Joe Manthey for discussions of woodpecker genomics. We thank Brant Faircloth and an anonymous reviewer for comments that improved our manuscript.
Publisher Copyright:
Copyright © 2020 Wiley et al.
PY - 2020/6/1
Y1 - 2020/6/1
N2 - 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.
AB - 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.
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U2 - 10.1534/g3.120.401059
DO - 10.1534/g3.120.401059
M3 - Article
C2 - 32317270
AN - SCOPUS:85085904995
VL - 10
SP - 1829
EP - 1836
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
SN - 2160-1836
IS - 6
ER -