@article{BanksNishiyamaHasebeetal.2011,
  author    = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  title     = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants},
  series = {Science},
  volume    = {332},
  journal   = {Science},
  number    = {6032},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.1203810},
  pages     = {960 -- 963},
  year      = {2011},
  abstract  = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  language  = {en}
}
@article{ChipmanFerrierBrenaetal.2014,
  author    = {Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schroeder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutierrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldon, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigo, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, Francois and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sanchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen},
  title     = {The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima},
  series = {PLoS biology},
  volume    = {12},
  journal   = {PLoS biology},
  number    = {11},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1545-7885},
  doi       = {10.1371/journal.pbio.1002005},
  pages     = {24},
  year      = {2014},
  abstract  = {Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.},
  language  = {en}
}