ArticlePloS one2014
Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana).G3 (Bethesda, Md.) · 2026Article
- Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories.PLoS neglected tropical diseases · 2024Article
- Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios.Frontiers in plant science · 2023Article
- Matamatas Chelus spp. (Testudines, Chelidae) have a remarkable evolutionary history of sex chromosomes with a long-term stable XY microchromosome system.Scientific reports · 2022Article
- The relevance of pedigrees in the conservation genomics era.Molecular ecology · 2022Article
- PromethION Sequencing and Assembly of the Genome of Micropoecilia picta, a Fish with a Highly Degenerated Y Chromosome.Genome biology and evolution · 2021Article
- The Amazonian Red Side-Necked TurtleCells · 2020Article
- Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.).Genome biology and evolution · 2019Article
- Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse.Scientific reports · 2019Article
- Article
- Reference-guided de novo assembly approach improves genome reconstruction for related species.BMC bioinformatics · 2017Article
- Genomics of coloration in natural animal populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Targeted Capture of Complete Coding Regions across Divergent Species.Genome biology and evolution · 2017Article
- Developing informative microsatellite markers for non-model species using reference mapping against a model species' genome.Scientific reports · 2016Article
- Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.PloS one · 2014Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
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