The genome of Darwin’s Finch (Geospiza fortis).

Dataset type: Genomic
Data released on August 03, 2012

Li B; Li H; Parker P; Wang J (2012): The genome of Darwin’s Finch (Geospiza fortis). GigaScience. http://dx.doi.org/10.5524/100040

DOI10.5524/100040

The Medium Ground Finch Geospiza fortis, is one of species of finches first collected by Charles Darwin on the Galapagos islands, and is emblematic for its involvement in the development of evolutionary theory by Darwin and for confirming the action of natural selection. Also know as a Darwin finch, we have sequenced a female individual at 115X coverage of HiSeq data, and produced a high quality draft genome assembly. The genome size of Geospiza fortis is at about 1.07 Gb. The scaffold N50 size of this assembly is at about 5.2Mb and contig N50 size is about 30Kb. A total of 16,286 protein coding genes were annotated. As well as being a model for the study of evolutionary biology, the availability of this genome will also be helpful for the subsequent population studies of this species. As another songbird genome, this will allow researchers to validate the findings of vocal learning gene and behavior interaction that has been carried out in the previously studied zebra finch.

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451

Accessions (data included in GigaDB):

GENBANK: AKZB00000000
BioProject: PRJNA156703

Accessions (data not in GigaDB):

SRA: SRA051234

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Geospiza fortis48883Darwin finchmedium ground-finchGeospiza fortis
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Geospiza fortisCoding sequenceFASTA6.93 MB2012-08-03
Geospiza fortisAnnotationGFF1.67 MB2012-08-03
Geospiza fortisProtein sequenceFASTA4.59 MB2012-08-03
Geospiza fortisSequence assemblyFASTA284.25 MB2012-08-03
ReadmeTEXT0.39 KB2012-08-03
Displaying 1-5 of 5 File(s).
Date Action
October 28, 2015 File Geospiza_fortis.gene.cds.gz updated
October 28, 2015 File Geospiza_fortis.gene.gff.gz updated
October 28, 2015 File Geospiza_fortis.gene.cds.gz updated
October 28, 2015 File Geospiza_fortis.scaf.noBacterial.fa.gz updated