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1.  The genomic substrate for adaptive radiation in African cichlid fish 
Brawand, David | Wagner, Catherine E. | Li, Yang I. | Malinsky, Milan | Keller, Irene | Fan, Shaohua | Simakov, Oleg | Ng, Alvin Y. | Lim, Zhi Wei | Bezault, Etienne | Turner-Maier, Jason | Johnson, Jeremy | Alcazar, Rosa | Noh, Hyun Ji | Russell, Pamela | Aken, Bronwen | Alföldi, Jessica | Amemiya, Chris | Azzouzi, Naoual | Baroiller, Jean-François | Barloy-Hubler, Frederique | Berlin, Aaron | Bloomquist, Ryan | Carleton, Karen L. | Conte, Matthew A. | D'Cotta, Helena | Eshel, Orly | Gaffney, Leslie | Galibert, Francis | Gante, Hugo F. | Gnerre, Sante | Greuter, Lucie | Guyon, Richard | Haddad, Natalie S. | Haerty, Wilfried | Harris, Rayna M. | Hofmann, Hans A. | Hourlier, Thibaut | Hulata, Gideon | Jaffe, David B. | Lara, Marcia | Lee, Alison P. | MacCallum, Iain | Mwaiko, Salome | Nikaido, Masato | Nishihara, Hidenori | Ozouf-Costaz, Catherine | Penman, David J. | Przybylski, Dariusz | Rakotomanga, Michaelle | Renn, Suzy C. P. | Ribeiro, Filipe J. | Ron, Micha | Salzburger, Walter | Sanchez-Pulido, Luis | Santos, M. Emilia | Searle, Steve | Sharpe, Ted | Swofford, Ross | Tan, Frederick J. | Williams, Louise | Young, Sarah | Yin, Shuangye | Okada, Norihiro | Kocher, Thomas D. | Miska, Eric A. | Lander, Eric S. | Venkatesh, Byrappa | Fernald, Russell D. | Meyer, Axel | Ponting, Chris P. | Streelman, J. Todd | Lindblad-Toh, Kerstin | Seehausen, Ole | Di Palma, Federica
Nature  2014;513(7518):375-381.
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
PMCID: PMC4353498  PMID: 25186727
2.  ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads 
Genome Biology  2009;10(10):R103.
Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).
PMCID: PMC2784318  PMID: 19796385

Results 1-2 (2)