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Comparative Genomics

 

  • Avian Genomes Database: This is a database under development, for genomes being built for songbirds and other species (hosted by the Jarvis Lab).

 

  • Brazillian Avian Genomics Project: SisbioAves: Phylogenomics, speciation, conservation and neuronal gene networks associated with song learning and speech/vocal imitation in Brazilian avian species (songbirds, hummingbirds and parrots). This consortium involves institutions in Brazil (Federal Universities of Brasilia, São Paulo, Minas Gerais, Pará and Rio Grande do Norte), USA (OHSU, Harvard Univ. and Duke Univ.) and UK (Roslin Inst./Univ. of Edinburgh, Scotland) and addresses avian biodiversity in Brazil, focusing on species that are of relevance for understanding the neural basis and evolution of vocal learning. The main goals are to 1) generate integrated ornithological collections, databases and tissue banks of avian species endemic and prevalent in Brazil, including threatened/endangered birds; 2) sequence, assemble and annotate the genomes of 5-7 avian species of relevance to vocal learning, including Turdus rufiventris (seasonal oscine), Amazona aestiva (true parrot), Pitangus sulphuratus (kiskadee/tyrannidae suboscine); 3) identify molecular markers of vocal control circuitry of vocal learning species; 4) generate data to help clarify avian phylogeny; 5) contribute to studies of avian phylogeography and speciation in the tropics; 6) develop capability of bioinformatics applied to genomics of complex organisms in Brazil. Co-PIs: Claudio Mello (OHSU, Portland OR, USA), Paula Schneider (Federal University of Pará, Belem PA, Brazil). Funded by the CNPq/MCT (Brazilian National Council for Research and Ministry of Science and Technology - 01/01/11 to 12/31/13)

  • Genome 10K and the Avianphylogenomics Initiative. This is a group has sequenced genomes of over 50 avian species, including known vocal learners (songbirds, parrots, and hummingbirds), and their close relatives (suboscine songbirds, falcons, and swifts). The goal is to sequence at least one species belonging to each major order for the following purposes: 1) Perform phylogenomic analyses to decipher avian phylogeny; 2) Identify genetic changes as signatures of convergent selection, including in vocal learning species; 3) Sequence genomes of avian species that provide scientific value to the community,  are national symbols, or endangered; and 4) Provide a public resource for scientist. The project is partnered with other initiatives such as the genome 10,000 (G10K) group to sequencing 10,000 vertebrate species in 10 years, a Copenhagen phylogenome group to decipher avian phylogeny, and the Beijing Genome Institute (BGI) to also decipher avian phylogeny and provide genomic resources. The project is coordinated by Erich Jarvis (Duke), Tom Gilbert (Copenhagen), and Goujie Zhang (BGI). Most of the funds come from BGI, with additional support from other groups.

GROUP SPECIES (sorted alphabetic) COMMON NAME FUND SOURCE STEWARDS SAMPLE SOURCES ORDER (Hacket & others)
Public HIGH COVERAGE GENOMES          
PUB Gallus gallus Chicken (Red jungle fowl) NIH Hillier et al 2004 Nature UCD001 line, Lee et al Anim Gene 2003 Galliformes
PUB Taeniopygia guttata Zebra finch NIH Warren et al 2010 Nature Art Arnold (UCLA) Passeriformes - Passerida# (Suborder Passeri)
PUB Meleagris gallopavo Wild turkey Roche 454/Univ Minnesota/Utah Univ/Virginia Tech/USDA/NIH Dalloul et al 2010 PloS Biology Nicholas inbred, Chavis et al 2009 Anim Genet Galliformes
PUB Melopsittacus undulatus Budgerigar (parakeet) Duke/HHMI/NIH/454/BGI/Pacbio Erich Jarvis (Duke Univ) Erich Jarvis (Duke Univ) Psittaciformes#
PUB Gymnogyps californianus California condor   Stephan Schuster (Penn State) Oliver Ryder (San Diego Zoo) Accipitriformes*
BGI-collab            
BGI Anas platyrhynchos domestica Peking duck China Agriculctural University Ling Li &BGI   Anseriformes
BGI Anser anser domesticus Domestic goose Zhejiang Academy of Agriculctural Sciences Lizhi Lu &BGI   Anseriformes
BGI Aptenodytes forsteri Emperor penguin BGI BGI   Spenisciformes* (SibAlq - Ciconiiformes)
BGI Columba livia Domestic pigeon BGI, Copenhagen Tom Gilbert   Columbiformes
BGI Egretta garzetta Little egret BGI     Ciconiiformes*
BGI Falco cherrug Saker falcon Cardiff Mike Bruford   Falconiformes*# (SibAlq - Ciconiiformes)
BGI Falco peregrinus Peregrine falcon Cardiff Mike Bruford   Falconiformes*# (SibAlq - Ciconiiformes)
BGI Nipponia nippon Crested Ibis Xian Jiaotong University Shengbin Li & BGI   Ciconiiformes*
BGI Pygoscelis adeliae Adelie penguin BGI David Lambert & BGI   Spenisciformes*(SibAlq - Ciconiiformes)
G10K-BGI            
G10K Calypte anna Anna's hummingbird BGI Erich Jarvis Claudio Mello OHSU Apodiformes - Trochilidae# (trochilinae)
G10K Chaetura pelagica Chimney swift BGI Erich Jarvis Elizabeth Derryberry - LSU Apodiformes - Apodidae#
G10K Charadrius vociferus Killdeer BGI Erich Jarvis Elizabeth Derryberry -LSU Charadriiformes (SibAlq - Ciconiiformes)
G10K Corvus brachyrhynchos American Crow BGI Erich Jarvis Halley Buckanoff - Ashboro NC Zoo Passeriformes - Passerida# (Family Corvidae)
G10K Cuculus canorus Common Cuckoo BGI Tom Gilbert & Erich Jarvis Jon Fjeldså -SNM Cuculiformes*#
G10K Geospiza fortis Medium ground finch BGI Oliver Ryder (San Diego Zoo) Patty Parker, Peter & Rosemary Grant Passeriformes - Passerida# (Suborder Passeri)
G10K Haliaeetus leucocephalus Bald Eagle NIH/Wash U Erich Jarvis Dave Scott - NC Rapture Center Accipitriformes*
G10K Manacus vitellinus Golden-collared Manakin BGI Erich Jarvis Barney Schlinger - UCLA Passeriformes - Suboscine# (Suborder Tyranni)
G10K Ophisthocomus hoazin Hoatzin BGI/New Mex State Univ Erich Jarvis & Peter Houde Peter Houde  Univ New Mexico; Elizabeth Derryberry - LSU Opisthocomiformes*
G10K Picoides pubescens Downy Woodpecker BGI Erich Jarvis Elizabeth Derryberry -LSU Piciformes
G10K Struthio camelus Ostrich BGI Oliver Ryder (San Diego Zoo) Oliver Ryder Struthioniformes
G10K Tinamus guttatus White throated tinamou BGI Erich Jarvis Elizabeth Derryberry -LSU Tinamiformes
  LOW COVERAGE GENOMES          
Copenhagen-BGI            
CH/BGI Acanthisitta chloris Rifleman BGI Tom Gilbert Mike Bunce Passerine suborder Acanthisitti
CH/BGI Apaloderma vittatum Bar-tailed trogon BGI Tom Gilbert Jon Fjeldså - SNM freezer Trogoniformes
CH/BGI Balearica regulorum gibbericeps Crowned crane BGI Tom Gilbert Copenhagen Zoo Gruiformes           
CH/BGI Buceros rhinoceros silvestris Javan rhinoceros hornbill BGI Tom Gilbert Copenhagen Zoo Coraciiformes - disputed. Some say Bucerotiformes
CH/BGI Caprimugus Carolinensis Chuk-will's-widow BGI Erich Jarvis Elizabeth Derryberry -LSU Caprimulgiformes           
CH/BGI Cariama cristata Red-legged seriema BGI Tom Gilbert Copenhagen Zoo ex Gruiformes*
CH/BGI Cathartes aura Turkey vulture BGI Erich Jarvis Dave Scott - NC Rapture Center Cathartidae*
CH/BGI Chlamydotis undulata Houbara  bustard BGI Tom Gilbert Tom Bailey - Dubai Falcon Hospital ex-Gruiformes*
CH/BGI Colius striatus Speckled mousebird BGI Tom Gilbert Copenhagen Zoo Coliiformes            
CH/BGI Eurypyga helias Sunbittern BGI Erich Jarvis Elizabeth Derryberry -LSU ex-Gruiformes* 
CH/BGI Fulmarus glacialis Northern Fulmar BGI Tom Gilbert Jon Fjeldså - SNM freezer Procellariformes (SibAlq - Ciconiiformes)        
CH/BGI Gavia stellata Red throated loon BGI Tom Gilbert Jon Fjeldså - SNM freezer Gaviiformes (SibAlq - Ciconiiformes)     
CH/BGI Haliaeetus albicilla White tailed eagle BGI Tom Gilbert Jon Fjeldså - SNM freezer Accipitriformes*
CH/BGI Leptosomus discolor Cuckoo roller BGI Tom Gilbert & Erich Jarvis Andreas Frei, Weltvogelpark Coraciiformes traditionally
CH/BGI Merops nubicus Northern Carmine bee-eater BGI Tom Gilbert Copenhagen Zoo Coraciiformes           
CH/BGI Mesitornis unicolor Brown mesite BGI Erich Jarvis & Tom Gilbert David Williard - Chicago Field Museum) ex-Gruiformes*      
CH/BGI Nestor notabilis Kea BGI Tom Gilbert Copenhagen Zoo Psittaciformes - most basal
CH/BGI Pelecanus crispus Dalmatian pelican BGI Tom Gilbert Copenhagen Zoo Pelecaniformes (SibAlq - Ciconiiformes)       
CH/BGI Phaethon lepturus White-tailed tropicbird BGI Tom Gilbert SNM freezer, Jon Fjeldså Phaethontiformes (traditionally Pelicaniformes)
CH/BGI Phalacrocorax carbo Great black cormorant BGI Tom Gilbert SNM freezer, Jon Fjeldså Pelicaniformes (SibAlq - Ciconiiformes)
CH/BGI Phoenicopterus ruber ruber Caribbean flamingo BGI Tom Gilbert Copenhagen Zoo Phoenicopteriformes
CH/BGI Podiceps cristatus Great-crested grebe BGI Tom Gilbert SNM freezer, Jon Fjeldså Podicipediformes (SibAlq - Ciconiiformes)    
CH/BGI Pterocles gutturalis Yellow-throated sandgrouse BGI Tom Gilbert An Pas, Sharjah Breeding Center Pteroclididae (SibAlq - Ciconiiformes, formerly Columbidae)
CH/BGI Tauraco erythrolophus Angola turaco BGI Tom Gilbert Copenhagen Zoo Musophagiformes by SibAlq, traditionally Cuculiformes         
CH/BGI Tyto alba Barn owl BGI Erich Jarvis Knudsen lab (Standford) Strigiformes           

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