Progress & News

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Publication

  • Hanada, K; Zhang, X; Borevitz, JO; Li, WH; Shiu, SH, "A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection", GENOME RESEARCH, p. 632, vol. 17, (2007).
  • Sahli, HF; Conner, JK, "Visitation, effectiveness, and efficiency of 15 genera of visitors to wild radish, Raphanus raphanismum (Brassicaceae)", AMERICAN JOURNAL OF BOTANY, p. 203, vol. 94, (2007).
  • Conner, JK, "A tale of two methods: putting biology before statistics in the study of phenotypic evolution", JOURNAL OF EVOLUTIONARY BIOLOGY, p. 17, vol. 20, (2007).
  • Knapczyk, F.N. and J.K. Conner, "Estimates of the average strength of natural selection are not inflated by sampling error or publication bias.", American Naturalist, p. 501, vol. 170, (2007).
  • Rensing, SA; Lang, D; Zimmer, AD; Terry, A; Salamov, A; Shapiro, H; Nishiyama, T; Perroud, PF; Lindquist, EA; Kamisugi, Y; Tanahashi, T; Sakakibara, K; Fujita, T; Oishi, K; Shin-I, T; Kuroki, Y; Toyoda, A; Suzuki, Y; Hashimoto, S; Yamaguchi, K; Sugano, S;, "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants", SCIENCE, p. 64, vol. 319, (2008).
  • Hanada, K; Zou, C; Lehti-Shiu, MD; Shinozaki, K; Shiu, SH, "Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli", PLANT PHYSIOLOGY, p. 993, vol. 148, (2008).
  • Shiu, SH; Borevitz, JO, "The next generation of microarray research: Applications in evolutionary and ecological genomics", HEREDITY, p. 141, vol. 100, (2008).
  • Sahli, HF; Conner, JK; Shaw, FH; Howe, S; Lale, A, "Adaptive Differentiation of Quantitative Traits in the Globally Distributed Weed, Wild Radish (Raphanus raphanistrum)", GENETICS, p. 945, vol. 180, (2008).
  • Franks, SJ; Avise, JC; Bradshaw, WE; Conner, JK; Etterson, JR; Mazer, SJ; Shaw, RG; Weis, AE, "The Resurrection Initiative: Storing Ancestral Genotypes to Capture Evolution in Action", BIOSCIENCE, p. 870, vol. 58, (2008).
  • Roles, AJ; Conner, JK, "Fitness effects of mutation accumulation in a natural outbred population of wild radish (raphanus raphanistrum): Comparison of field and greenhouse environments", EVOLUTION, p. 1066, vol. 62, (2008).
  • Duffy, MA; Brassil, CE; Hall, SR; Tessier, AJ; Caceres, CE; Conner, JK, "Parasite-mediated disruptive selection in a natural Daphnia population", BMC EVOLUTIONARY BIOLOGY, p. , vol. 8, (2008).
  • Lehti-Shiu, M. D.;Zou, C.;Hanada, K.;Shiu, S. H.;, "Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes", Plant Physiol, p. 12-26, vol. 150, (2009).
  • Zou, C.;Lehti-Shiu, M. D.;Thomashow, M.;Shiu, S. H.;, "Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana", PLoS Genet, p. e1000581, vol. 5, (2009).
  • Conner, Jeffrey K.;Sahli, Heather F.;Karoly, Keith;, "Tests of adaptation: functional studies of pollen removal and estimates of natural selection on anther position in wild radish", Ann Bot, p. 1547-1556, vol. 103, (2009).
  • Lin H, Moghe G, Ouyang S, Iezzoni A, Shiu SH, Gu X, Buell CR (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol 10:41.
  • Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH (2010) sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics 26(3):399.
  • Sahli, H. and J.K. Conner, "Testing for conflicting and non-additive selection: floral adaptation to multiple pollinators through male and female fitness", Evolution, p. 1427, vol. 65, (2011).
  • Conner, J.K., Karoly, K., Stewart, C., Koelling, V.A., Sahli, H.F., and Shaw, F.H. 2011. Rapid Independent Trait Evolution Despite a Strong Pleiotropic Genetic Correlation. American Naturalist 178: 429-441. (lead article)
  • Hua Z, Zou C, Shiu SH, Vierstra RD (2011) Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift. PLoS ONE 6(1):e16219.
  • Rutter, M.T., A. Roles, J.K. Conner, R.G. Shaw, F.H. Shaw, K. Schneeberger, S. Ossowski, D. Weigel, C.B. Fenster. 2012. Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known. In press, Evolution.
  • Lehti-Shiu MD, Shiu SH (2012) Diversity and Function of the Protein Kinase Superfamily in Plants. Philos Trans R Soc Lond B Biol Sci [in press].


2012

  • March: Radish draft annotation finished.

2011

  • September: Shotgun sequencing of radish genome finished. First draft assembly generated.

2008

11:48, 26 May 2008 (EDT)

  • Computationally identified SSRs are deposited here.

14:38, 7 April 2008 (EDT)

  • Email sent to over 500 researchers announcing the availability of radish cDNA sequences and the community forum.

16:11, 13 March 2008 (EDT)

  • Sequencing phase finished. 7 libraries were sequenced with ~25,000 clones each. GenBank now has 287336 radish ESTs. Current we are identifying the full length clone and preparing for depositing radish EST clones to ABRC.
  • In addition to EST contigs generated by JCVI, radish EST sequences have been incorporated into PlantGDB where you can download EST contigs of various radish species/subspecies.

2007

16:01, 3 December 2007 (EDT)

  • 57270 additional sequences submitted to GenBank.

12:42, 31 October 2007 (EDT)

  • 23698 additional sequences submitted to GenBank.

09:58, 22 August 2007 (EDT)

  • 26307 additional sequences submitted to GenBank.

09:26, 19 July 2007 (EDT)

  • First batch sequencing done. We have sequenced on both ends from about 5000 clones from CS, MS, NY and PB libraries (R. raphanistrum) and about 2500 clones from both ends from AR, RS and RT libraries (R.sativus).
  • Preparation for GenBank submission.
  • Preparation for sending dear colleague email to the radish research community.

11:24, 30 May 2007 (EDT)

  • The sequences from the testblocks of our seven libraries are finished and they are good.

12:00, 11 April 2007 (EDT)

  • cDNA libraries ready.
  • Sequencing started in JCVI.

13:30, 17 March, 2007 (EDT)

  • ELPL outreach activity.

12:00, 1 January 2007 (EDT)

  • RNA isolation completed.

2006

12:00, 1 December 2006 (EDT)

  • Project funding available.
  • RadishDB online.
  • Growing plant materials.