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.
Sage-Grouse de novo assembly
De novo assembly of the Gunnison Sage-Grouse using CLC Genomics Workbench. Includes CLC assembly report.
Sage_Grouse_denovo_assembly_07-17-2013_DCC.tar.bz2
Clark's Nutcracker de novo assembly
De novo assembly of the Clark's Nutcracker using CLC Genomics Workbench. Includes CLC assembly report.
Clarks_Nutcracker_denovo_assembly_07-17-2013_DCC.tar.bz2
Sage-Grouse to Chicken chromosome annotation
Chromsome annotation of the Sage-Grouse using the Chicken genome. Used 1x reference-guided assembly and blast, and assumed high synteny between species.
SG_chrs.tar.bz2
Clark's Nutcracker to Zebra Finch chromosome annotation
Chromosome annotation of the Clark's Nutcracker using the Zebra Finch genome. Used 1x reference-guided assembly and blast, and assumed high synteny between species.
CN_chrs.tar.bz2
Sage-Grouse 1x reference-guided genome
1x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
SG_1x_guided_consensus.tar.bz2
Sage-Grouse 2x reference-guided genome
2x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
SG_2x_guided_consensus.tar.bz2
Sage-Grouse 5x reference-guided genome
5x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
SG_5x_guided_consensus.tar.bz2
Sage-Grouse mitochondrial assembly and MITOS annotation
Reference-guided assembly of the Sage-Grouse mitochondrion using consensus Galliformes mitochondrial sequence as guide. Includes MITOS annotation.
SG_MITOS_MtGenomes_Annotation.tar.bz2
Clark's Nutcracker 1x reference-guided genome
1x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
CN_1x_guided_consensus.tar.bz2
Clark's Nutcracker 2x reference-guided genome
2x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
CN_2x_guided_consensus.tar.bz2
Clark's Nutcracker 5x reference-guided genome
5x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
CN_5x_guided_consensus.tar.bz2
Clark's Nutcracker mitochondrial assembly and MITOS annotation
Reference-guided assembly of the Clark's Nutcracker mitochondrion using consensus Corvidae mitochondrial sequence as guide. Includes MITOS annotation.
CN_MITOS_MtGenomes_Annotation.tar.bz2