ACCOMPLISHMENTS AND PUBLICATIONS
Research and publication accomplishment highlights from our consortium members
Vertebrate Genomes Project Publications
COVID-19 Research
Variation in predicted COVID-19 risk among lemurs and lorises
Melin, et al. April 1, 2021; Am J Primatol.
Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
Damas, Hughes, et al. April 18, 2020; bioRxiv.
Methods
The era of reference genomes in conservation genomics
Formenti et al. January 24, 2022; Trends in Ecology & Evolution.
The Earth BioGenome Project 2020: Starting the clock
Lewin et al. January 18, 2022; PNAS.
Robust haplotype-resolved assembly of diploid individuals without parental data
Cheng et al. September 10, 2021; arXiv.
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
Dahn et al. July 20, 2021; bioRxiv.
Merfin: improved variant filtering and polishing via k-mer validation
Formenti et al. July 18, 2021; bioRxiv.
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, MacCarthy, Fedrigo et al. April 28, 2021; Nature.
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C Kronenberg et al. April 28, 2021; Nature Comunications.
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Formenti et al. April 29, 2021; Genome Biology.
False gene and chromosome losses affected by assembly and sequence errors
Kim et al. April 9, 2021; bioRxiv.
Significantly improving the quality of genome assemblies through curation
Howe et al. January 9, 2021; GigaScience.
Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species
Morin et al. 2020; Mar Mam Sci.
Reference Genomes
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
Mueller et al. December 20, 2021; GigaScience.
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
Toh et al. December 10, 2021; bioRxiv.
Population genomics of the critically endangered kākāpō
Dussex et al. 2021; Cell Genomics.
Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution
Peart et al. June 7, 2021; Molecular Ecology Resources.
The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 3 approved].
Hansen et al. 2021; Wellcome Open Res.
Reference genome and demographic history of the most endangered marine mammal, the vaquita
Morin et al. Oct 22, 2020; Molecular Ecology Resources.
Six reference-quality genomes reveal evolution of bat adaptations Jebb et al. July 22, 2020; Nature.
The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758 [version 1; peer review: 2 approved].
Mead et al. 2020; Wellcome Open Res.
SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)
Formenti et al. Jan 1, 2019; Gigascience.
Biological Discoveries
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
Lovell et al. September 9, 2022; eLife.
Recombination suppression and selection affect local ancestries in genomes of a migratory songbird
Ishigohoka et al. December 23, 2021; bioRxiv.
Universal nomenclature for oxytocin-vasotocin ligand and receptor families Theofanopoulou et al. April 28, 2021; Nature.
Evolutionary and biomedical insights from a marmoset diploid genome assembly Yang et al. April 28, 2021; Nature.
Platypus and echidna genomes reveal mammalian biology and evolution Zhou et al. January 6, 2021; Nature.
Conservation
Reference Genomes for Conservation
Paez, Kraus et al. July 22, 2022; Science. ( Supplementary Materials )
Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life historie
Bentley et al. January 18, 2022; bioRxiv.
Previous Accomplishments
A competitive assessment of de novo short-read assembly methods; simulation of sequence based on human Chromosome 13.
A competitive assessment using de novo methods of genome assembly in three vertebrate species (i.e., bird, snake, and fish); one outcome was PBJelly gap-filling tool.
A competitive assessment of whole-genome alignment methods.
101 GENOMES PROJECT (with BGI)
In 2010, BGI partnered with G10K to sequence the first 101 species, with representatives from each vertebrate group.
Avian Phylogenomics Project (APP)
The Avian Phylogenomics Project (APP), led by Drs. Jarvis, Zhang, and Gilbert, included over 200 researchers from 80 institutions in 20 countries and successfully sequenced the genomes of birds in all 40+ orders, including 7 endangered species with DNA isolated from frozen tissue samples.
Select Publications
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10,000 Vertebrate Species
J Hered. 2009 Nov 4;100:659-674.
Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds
Science. 12 Dec 2014;346(6215): 1320-31.
Comparative Genomics Reveals Insights Into Avian Genome Evolution and Adaptation
Science. 12 Dec 2014;346(6215): 1311-20
The Genome 10K Project: A Way Forward
Annual Review of Animal Biosciences. 2015;3:57-111.
Prior VGP Member Accomplishments
Leadership of the G10K help develop the BLAST algorithm widely used by the scientific community
Members from the B10K have successfully conducted large-scale international genome projects. The B10K aims to generate representative draft genome sequences from all extant bird species.
The Bat1K aims to generate reference genomes of all living (~1300) bat species and contribute them to the VGP effort.
Several members of the VGP leadership previously co-led the first human genomes project and the current 1000 human genomes project.
Members of the VGP leadership include those co-leading the Global Alliance for Genomics and Health (GAGH)
The Earth Biogenome Project, to which the VGP will contribute genomes.
100&Change grant mechanism: our proposal was shortlisted as one of the top ten of all proposals
