G10k Publications

These are selected publications from Genome 10K leadership. For publications from G10K colleagues, see our Community Member Publications.

Hughes, L.C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C.C., Thompson, A.W., Arcila, D., Betancur-R, R., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B, Zhou, Z., Huang, H., Chen, S., Venkatesh, B. and Shi, Q. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc. Natl. Acad. Sci. USA. (2018) 115: 6249-6254.

Harris A. Lewin, Gene E. Robinson, W. John Kress, William J. Baker, Jonathan Coddington, Keith A. Crandall, Richard Durbin, Scott V. Edwards, Félix Forest, M. Thomas P. Gilbert, Melissa M. Goldstein, Igor V. Grigoriev, Kevin J. Hackett, David Haussler, Erich D. Jarvis, Warren E. Johnson, Aristides Patrinos, Stephen Richards, Juan Carlos Castilla-Rubio, Marie-Anne van Sluys, Pamela S. Soltis, Xun Xu, Huanming Yang, Guojie Zhang Proceedings of the National Academy of Sciences Apr 2018, 201720115; DOI: 10.1073/pnas.1720115115

Add Novak Ben J., Estes James A., Shaw Holland E., Novak Erika V., Shapiro Beth. Experimental Investigation of the Dietary Ecology of the Extinct Passenger Pigeon, Ectopistes migratorius. rontiers in Ecology and Evolution. 6;2018.

Lin, Q., Venkatesh, B., et al. The seahorse genome and the evolution of its specialized morphology. Nature 540, 395–399 (15 December 2016)

Pan, H., Yu, H., Ravi, V., et al. The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate. GigaScience (2016) 5:36.

Bian, C., Venkatesh, B., et al. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci. Rep. (2016) 6: 24501.

Klaus-Peter Koepfli, Benedict Paten, the Genome 10K Community of Scientists, and Stephen J. O’Brien. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. 2015;3:57-111.

You, X., Venkatesh, B., et al. Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nat. Commun. (2014) 5:5594.

(See Avian Phylogenomics Project publications below)

Bradnam, KR, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22;2(1):10.

Wong PB, et al. Tissue sampling methods and standards for vertebrate genomics. GigaScience. 2012 Jul 12;1(1):8

Bernardi G, et al. The fishes of Genome 10K, Mar Genomics. 2012 Sep;7:3-6.

Earl D, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011. Dec;21(12):2224-41.

Genome 10K Community of Scientists. A proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov 4;100:659-674.

Avian Phylogenomics Project

Flagship papers

Zhang G, Li C, Qiye L, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 12 December 2014:346(6215):1311-20.

Jarvis ED, Mirarab S, Aberer AJ, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 12 December 2014;346(6215):1320-31.

 

Genome Evolution

Smeds, L., Qvarnstrom, A., Ellegren, H. Direct estimate of the rate of germline mutation in a bird. Genome Research. 16 July 2016 DOI: 10.1101/gr.204669.116

Smeds, L., Mugal, C.F., Qvarnstrom, A., Ellegren, H. High-resolution mapping of crossover and non-crossover recombination events by whole-genome re-sequencing of an avian pedigree. PLoS Genetics. 24 May 2016 DOI: 10.1371/journal.pgen.1006044.

Chao Bian, Yinchang Hu, Qiong Shi, et al.The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleostsScientific Reports 6, Article number: 24501 (2016) doi:10.1038/srep24501

Uebbing, S., Kunstner, A., Makinen, H., Backstrom, N., Bolivar, P., Burri, R., Dutoit, L., Mugal, C.F., Nater, A., Aken, B., Flicek, P., Martin, F.J., Searle, S.M.J., Ellegren, H. Divergence in gene expression within and between two closely related flycatcher species. Molecular Ecology. 2 April 2016 DOI: 10.1111/mec.13596.

Figuet, E., Nabholz, B., Bonneau, M., Mas Carrio, E., Nadachowska-Brzyska, K., Ellegren, H., Galiter, N. Life history traits, protein evolution and the nearly-neutral theory in amniotes. Molecular Biology and Evolution. 4 March 2016 DOI: 10.1093/molbev/msw033.

Nadachowska-Brzyska, K., Burri, R., Smeds, L., Ellegren, H. PSMC-analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Molecular Ecology. 15 February 2016. DOI: 10.1111/mec.13540

Bolivar, P., Mugal, C.F. Nater, A., Ellegren, H. Recombination rate variation modulates gene sequence evolution mainly via GC-biased gene conversion, not Hill-Robertson interference, in an avian system. Molecular Biology and Evolution. 6 October 2015. DOI: 10.1093/molbev/msv214.

Mugal, C.F., Weber, C.C., Ellegren, H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. BioEssays. 7 October 2016. DOI: 10.1002/bies.201500058.

Burri, R., Nater, A., Kawakami, T., Mugal, C.F., Olason, P.I., Smeds, L., Suh, A., Dutoit, L., Bures, S., Garamszegi, L.Z., Hogner, S., Moreno, J., Qvarnstrom, A., Ruzic, M., Saether, S.A., Saetre, G.P., Torok, J., Ellegren, H. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research. 9 September 2016. DOI:10.1101/gr.196485.115

Zhou Q, Zhang J, Bachtrog D, et al. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science. 12 December 2014:346(6215) DOI: 10.1126/science.1246338.

Cui J, Zhao W, Huang Z, et al. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biology. 11 December 2014:15(12):539.

Romanov MN, Farré M, Lithgow PE, et al. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics. 11 December 2014:15:1060.

Suh A, Churakov G, Ramakodi MP, et al. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol Evol. 11 December 2014:6(12) DOI: 10.1093/gbe/evu256

Weber CC, Nabholz B, Romiguier J, et al. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biology. 11 December 2014:15(12):542.

Weber CC, Boussau B, Romiguier J, et al. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biology. 11 December 2014:15(12):549.

 

Avian Biology

Li C, Zhang Y, Li J, et al. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. GigaScience. 12 December 2014:3:27

Shapiro MD, Kronenberg Z, Li C, et al. Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon. Science. 1 March 2013:339(6123):1063-1067.

Huang Y, Li Y, Burt DW, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet. 2013 Jul;45(7):776-83.

Zhan X, Pan S, Wang J, et al. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet. 2013 May;45(5):563-6.

Ganapathy G, Howard JT, Ward JM, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 2014 Jul 8;3:11.

Li S, Li B, Cheng C, et al. Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. Genome Biol. 2014 Dec 11;15(12):557.

Meredith RW, Zhang G, Gilbert MT, et al. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science. 2014 Dec 12;346(6215):1254390.

Greenwold MJ, Bao W, Jarvis ED,, et al. Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles.BMC Evol Biol. 2014 Dec 12;14:249.

Whitney O, Pfenning AR, Howard JT, et al. Core and region-enriched networks of behaviorally regulated genes and the singing genome.Science. 2014 Dec 12;346(6215):1256780.

Pfenning AR, Hara E, Whitney O, et al. Convergent transcriptional specializations in the brains of humans and song-learning birds.Science. 2014 Dec 12;346(6215):1256846.

Wang R, Chen CC, Hara E, et al. Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners.J Comp Neurol. 2014 Nov 26.

Parchman TL, Gompert Z, Braun MJ, et al. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins.Mol Ecol. 2013 Jun;22(12):3304-17.

 

Methodology

Dutoit, L., Burri, R., Nater, A., Mugal, C.F. & Ellegren, H. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology Resources. 2016 Nov 14 DOI: 10.1111/1755-0998.12602.

Kardos, M., Husby, A., McFarlane, S.E., Qvarnstrom, A., Ellegren, H. Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Molecular Ecology Resources. 24 December 2015 DOI:10.1111/1755-0998.12498.

Mirarab S, Bayzid MS, Boussau B, et al. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science. 2014 Dec 12;346(6215) DOI: 10.1126/science.1250463.

 

Others

Green RE, Braun ED, Armstrong J, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.. Science. 2014 Dec 12;346(6215) DOI: 10.1126/science.1254449.

Jaratlerdsiri W, Deakin J, Godinez RM, et al. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLOS One. 2014 Dec 11 DOI: 10.1371/journal.pone.0114631.

Chong AY, Kojima KK, Jurka J, et al. Evolution and gene capture in ancient endogenous retroviruses – insights from the crocodilian genomes.. Retrovirology. 2014 Dec 12;11:71.

Zhang G, Li B, Li C, et al. Comparative genomic data of the Avian Phylogenomics Project. GigaScience. 2014 Dec 11;3:26.

OBrien SJ, Haussler D, Ryder O. The birds of Genome 10K. GigaScience. 2014 Dec 11;3:32.