Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies
PLoS ONE
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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.
Suggested Citation
Card, D., Schield, D., Reyes-Velasco, J., Fujita, M.K., Andrew, A., Oyler-McCance, S.J., Fike, J., Tomback, D.F., Ruggiero, R.P., and Castoe, T.A., 2014, Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies: PLoS ONE, v. 9, no. 9, e106649; 13 p., https://doi.org/10.1371/journal.pone.0106649.
| Publication type | Article |
|---|---|
| Publication Subtype | Journal Article |
| Title | Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies |
| Series title | PLoS ONE |
| DOI | 10.1371/journal.pone.0106649 |
| Volume | 9 |
| Issue | 9 |
| Publication Date | September 05, 2014 |
| Year Published | 2014 |
| Language | English |
| Publisher | Public Library of Science |
| Contributing office(s) | Fort Collins Science Center |
| Description | e106649; 13 p. |
| Larger Work Type | Article |
| Larger Work Subtype | Journal Article |
| Larger Work Title | PLoS ONE |