Early fruits of the collaboration between the Genome 10K project and Beijing Genomics Institute (BGI) to sequence 100 vertebrate species have resulted in the sequencing and release of the genome of one of naturalist Charles Darwin's Galápagos finches, the medium ground finch Geospiza fortis.
This finch genome, the first of the BGI-Genome 10K collaboration to be made available through the UCSC Genome Browser, represents both a scientific and a symbolic advancement, according to Erich Jarvis, Duke University associate professor who studies the neurobiology of vocal learning in songbirds.
"The scientific advancement is that it will allow us to investigate the genomes of a group of closely related species with a significant amount of diversity on an island population, allowing us to potentially better understand the genetics of trait evolution," said Jarvis.
Endemic to the subtropical or tropical dry forests and shrublands of the Galápagos Islands this species evolves rapidly in response to environmental changes.
"These finches are of great historical significance, but when Darwin first studied these birds, he was unlikely to have envisioned how this species would become a perfect model to study evolution in action," said Goujie Zhang, BGI's associate director of research. "Having the reference genome of this species has opened the door for carrying out studies that can look at real-time evolutionary changes on a genomic level of all of these enigmatic species."
Scientists hope that the new genome will help them understand the evolution of vocal learning. The study includes genes with positively selected mutations involved with the vocal learning trait in finches and also with behavior necessary for spoken language in humans. Adding richness to the possibility of understanding the genomic components of vocal learning, researchers have been recording Geospiza songs over the last 40 years. These recordings reveal dialectic patterns that can now be linked to the genome by sequencing the genomes of additional individuals from living and past populations. In addition to its usefulness for investigating speciation, this genomic data can help in conservation efforts.
The medium ground finch genome, which is nearly one-third the size of the human genome, was sequenced from an individual female, producing a high-quality draft using 115X coverage next-generation sequencing data from an Illumina HiSeq sequencing system. With the aid of transcriptome data, BGI was able to annotate 16,286 protein-coding genes in this genome.
Oliver Ryder, director of genetics at the San Diego Zoo Institute for Conservation Research, placed the new genome in a larger context.
"The availability of this high-quality genome assembly produced by BGI will facilitate the stewardship of earth's biodiversity—a cherished goal of Genome10K," said Ryder.
The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.
The San Diego Zoo Global Wildlife Conservancy is dedicated to bringing endangered species back from the brink of extinction. The work of the Conservancy includes onsite wildlife conservation efforts at the San Diego Zoo, San Diego Zoo Safari Park, San Diego Zoo Institute for Conservation Research, and international field programs in more than 35 countries. In addition, San Diego Zoo Global manages the Anne and Kenneth Griffin Reptile Conservation Center, the Frozen ZooTM and Native Seed Gene Bank, the Keauhou and Maui Hawaii Endangered Bird Conservation Centers, San Clemente Loggerhead Shrike Breeding Facility, Cocha Cashu Biological Research Station, the Desert Tortoise Conservation Center, and a 900-acre biodiversity reserve adjacent to the San Diego Zoo Safari Park. The important conservation and science work of these entities is supported in part by The Foundation of the Zoological Society of San Diego.
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