Comparative Genomics

Comparative genomics is a powerful too to investigate the genetics of complex traits. We used comparative genomics to investigate the neurogenetics of vocal learning and spoken language.

Vocal learning is a remarkable rare convergent behavior, essential to spoken language. To gain new insights into the origins of vocal learning, and compare genetic similarities across all vocal learning lineages, we are generating and integrating data from a wide array of genome sequencing techniques (Bulk RNA-seq, snRNA-seq, ATAC-seq, whole-genome bisulfite-seq) and analyses to determine the molecular basis of vocal learning brain pathways in vocal learning birds (zebra finch, parrot) and mammals (humans, dolphins), and then contrast them with the pathways found in non-learning relatives (non-human primates, rodents, and chickens). This endeavor requires reference genomes with assemblies that are near error free, gapless, complete and correctly haplotype phased. We are working with the Vertebrate Genomes Project to generate improved protocols for genome assembly in order to produce such high quality genomes essential to our understanding of the genetic drivers of vocal learning. Furthermore, these assemblies will be an invaluable resource to the rest of the scientific community studying other complex traits across a wide variety of species.

How did vocal learning evolve?
Can we use reference genomes to understand vertebrate evolution?
Can the study of evolution help us preserve biodiversity for future generations?

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Further Readings

Towards complete and error-free genome assemblies of all vertebrate species. Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher Balakrishnan, Dave Burt, Julia M. George, Mathew Biegler, David Iorns, Andrew Digby, Daryl Eason, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J.P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Jonas Korlach, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H.S. Kraus, Harris Lewin, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Hausler, Stephen J. O'Brien, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, and Erich D. Jarvis Biorxiv https://doi.org/10.1101/2020.05.22.110833

Convergent transcriptional specializations in the brains of humans and song-learning birds. Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Science. 2014 Dec 12;346(6215):1256846.

Whole-genome analyses resolve early branches in the tree of life of modern birds. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. Science. 2014 Dec 12;346(6215):1320-31.

Comparative genomics reveals insights into avian genome evolution and adaptation. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. Science. 2014 Dec 12;346(6215):1311-20.

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