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1.  The dynamic genome of Hydra 
Chapman, Jarrod A. | Kirkness, Ewen F. | Simakov, Oleg | Hampson, Steven E. | Mitros, Therese | Weinmaier, Therese | Rattei, Thomas | Balasubramanian, Prakash G. | Borman, Jon | Busam, Dana | Disbennett, Kathryn | Pfannkoch, Cynthia | Sumin, Nadezhda | Sutton, Granger G. | Viswanathan, Lakshmi Devi | Walenz, Brian | Goodstein, David M. | Hellsten, Uffe | Kawashima, Takeshi | Prochnik, Simon E. | Putnam, Nicholas H. | Shu, Shengquiang | Blumberg, Bruce | Dana, Catherine E. | Gee, Lydia | Kibler, Dennis F. | Law, Lee | Lindgens, Dirk | Martinez, Daniel E. | Peng, Jisong | Wigge, Philip A. | Bertulat, Bianca | Guder, Corina | Nakamura, Yukio | Ozbek, Suat | Watanabe, Hiroshi | Khalturin, Konstantin | Hemmrich, Georg | Franke, André | Augustin, René | Fraune, Sebastian | Hayakawa, Eisuke | Hayakawa, Shiho | Hirose, Mamiko | Hwang, Jung Shan | Ikeo, Kazuho | Nishimiya-Fujisawa, Chiemi | Ogura, Atshushi | Takahashi, Toshio | Steinmetz, Patrick R. H. | Zhang, Xiaoming | Aufschnaiter, Roland | Eder, Marie-Kristin | Gorny, Anne-Kathrin | Salvenmoser, Willi | Heimberg, Alysha M. | Wheeler, Benjamin M. | Peterson, Kevin J. | Böttger, Angelika | Tischler, Patrick | Wolf, Alexander | Gojobori, Takashi | Remington, Karin A. | Strausberg, Robert L. | Venter, J. Craig | Technau, Ulrich | Hobmayer, Bert | Bosch, Thomas C. G. | Holstein, Thomas W. | Fujisawa, Toshitaka | Bode, Hans R. | David, Charles N. | Rokhsar, Daniel S. | Steele, Robert E.
Nature  2010;464(7288):592-596.
The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction.
doi:10.1038/nature08830
PMCID: PMC4479502  PMID: 20228792
2.  Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri 
Science (New York, N.Y.)  2010;329(5988):223-226.
The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138–mega–base pair genome of V. carteri and compared its ~14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal–specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.
doi:10.1126/science.1188800
PMCID: PMC2993248  PMID: 20616280
3.  The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions 
Merchant, Sabeeha S. | Prochnik, Simon E. | Vallon, Olivier | Harris, Elizabeth H. | Karpowicz, Steven J. | Witman, George B. | Terry, Astrid | Salamov, Asaf | Fritz-Laylin, Lillian K. | Maréchal-Drouard, Laurence | Marshall, Wallace F. | Qu, Liang-Hu | Nelson, David R. | Sanderfoot, Anton A. | Spalding, Martin H. | Kapitonov, Vladimir V. | Ren, Qinghu | Ferris, Patrick | Lindquist, Erika | Shapiro, Harris | Lucas, Susan M. | Grimwood, Jane | Schmutz, Jeremy | Cardol, Pierre | Cerutti, Heriberto | Chanfreau, Guillaume | Chen, Chun-Long | Cognat, Valérie | Croft, Martin T. | Dent, Rachel | Dutcher, Susan | Fernández, Emilio | Ferris, Patrick | Fukuzawa, Hideya | González-Ballester, David | González-Halphen, Diego | Hallmann, Armin | Hanikenne, Marc | Hippler, Michael | Inwood, William | Jabbari, Kamel | Kalanon, Ming | Kuras, Richard | Lefebvre, Paul A. | Lemaire, Stéphane D. | Lobanov, Alexey V. | Lohr, Martin | Manuell, Andrea | Meier, Iris | Mets, Laurens | Mittag, Maria | Mittelmeier, Telsa | Moroney, James V. | Moseley, Jeffrey | Napoli, Carolyn | Nedelcu, Aurora M. | Niyogi, Krishna | Novoselov, Sergey V. | Paulsen, Ian T. | Pazour, Greg | Purton, Saul | Ral, Jean-Philippe | Riaño-Pachón, Diego Mauricio | Riekhof, Wayne | Rymarquis, Linda | Schroda, Michael | Stern, David | Umen, James | Willows, Robert | Wilson, Nedra | Zimmer, Sara Lana | Allmer, Jens | Balk, Janneke | Bisova, Katerina | Chen, Chong-Jian | Elias, Marek | Gendler, Karla | Hauser, Charles | Lamb, Mary Rose | Ledford, Heidi | Long, Joanne C. | Minagawa, Jun | Page, M. Dudley | Pan, Junmin | Pootakham, Wirulda | Roje, Sanja | Rose, Annkatrin | Stahlberg, Eric | Terauchi, Aimee M. | Yang, Pinfen | Ball, Steven | Bowler, Chris | Dieckmann, Carol L. | Gladyshev, Vadim N. | Green, Pamela | Jorgensen, Richard | Mayfield, Stephen | Mueller-Roeber, Bernd | Rajamani, Sathish | Sayre, Richard T. | Brokstein, Peter | Dubchak, Inna | Goodstein, David | Hornick, Leila | Huang, Y. Wayne | Jhaveri, Jinal | Luo, Yigong | Martínez, Diego | Ngau, Wing Chi Abby | Otillar, Bobby | Poliakov, Alexander | Porter, Aaron | Szajkowski, Lukasz | Werner, Gregory | Zhou, Kemin | Grigoriev, Igor V. | Rokhsar, Daniel S. | Grossman, Arthur R.
Science (New York, N.Y.)  2007;318(5848):245-250.
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
doi:10.1126/science.1143609
PMCID: PMC2875087  PMID: 17932292
4.  Annotation of the Drosophila melanogaster euchromatic genome: a systematic review 
Genome Biology  2002;3(12):research0083.1-83.22.
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
Background
The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
Results
Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
Conclusions
Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
doi:10.1186/gb-2002-3-12-research0083
PMCID: PMC151185  PMID: 12537572

Results 1-4 (4)