Sat, 19 Jul 2008 00:43:46 BST CiteULike: neils's Thimmapuram http://www.citeulike.org/user/neils/author/Thimmapuram CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2709869 <i>Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996.</i> The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Ray Ming Shaobin Hou Yun Feng Qingyi Yu Alexandre Dionne-Laporte Jimmy Saw Pavel Senin Wei Wang Benjamin Ly Kanako Lewis Steven Salzberg Lu Feng Meghan Jones Rachel Skelton Jan Murray Cuixia Chen Wubin Qian Junguo Shen Peng Du Moriah Eustice Eric Tong Haibao Tang Eric Lyons Robert Paull Todd Michael Kerr Wall Danny Rice Henrik Albert Ming-Li Wang Yun Zhu Michael Schatz Niranjan Nagarajan Ricelle Acob Peizhu Guan Andrea Blas Ching Wai Christine Ackerman Yan Ren Chao Liu Jianmei Wang Jianping Wang Jong-Kuk Na Eugene Shakirov Brian Haas Jyothi Thimmapuram David Nelson Xiyin Wang John Bowers Andrea Gschwend Arthur Delcher Ratnesh Singh Jon Suzuki Savarni Tripathi Kabi Neupane Hairong Wei Beth Irikura Maya Paidi Ning Jiang Wenli Zhang Gernot Presting Aaron Windsor Rafael Navajas-Perez Manuel Torres Alex Feltus Brad Porter Yingjun Li Max Burroughs Ming-Cheng Luo Lei Liu David Christopher Stephen Mount Paul Moore Tak Sugimura Jiming Jiang Mary Schuler Vikki Friedman Thomas Mitchell-Olds Dorothy Shippen Claude Depamphilis Jeffrey Palmer Michael Freeling Andrew Paterson Dennis Gonsalves Lei Wang Maqsudul Alam doi:10.1038/nature06856 Nature, Vol. 452, No. 7190. (24 April 2008), pp. 991-996. 2008-04-23T19:37:29-00:00 2008 Nature 452 7190 991 996 Nature Publishing Group genome genomics papaya plant sequence http://www.citeulike.org/user/neils/article/2553355 <i>BMC Genomics, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.RESULTS:We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in ESTIMA:Songbird. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a aCommunity Collaborationa mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.CONCLUSIONS:Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve. The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution Kirstin Replogle Arthur Arnold Gregory Ball Mark Band Staffan Bensch Eliot Brenowitz Shu Dong Jenny Drnevich Margaret Ferris Julia George George Gong Dennis Hasselquist Alvaro Hernandez Ryan Kim Harris Lewin Lei Liu Peter Lovell Claudio Mello Sara Naurin Sandra Zas Jyothi Thimmapuram Juli Wade David Clayton doi:10.1186/1471-2164-9-131 BMC Genomics, Vol. 9, No. 1. (2008) 2008-03-19T00:14:12-00:00 2008 BMC Genomics 9 1 annotation bioinformatics bird genome genomics zebrafinch