Identifying Eucalyptus expressed sequence tags related to Arabidopsis flowering-time pathway genes

RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.)

Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is widely used for early spring grazing in western Canada and the development of late maturing cultivars which maintain forage quality for a longer period is desired. However, it is difficult to manipulate the timing of floral transition, as little is known about molecular mechanism of plant maturity in this species. In this study, RNA-Seq and differential gene expression analysis were performed to investigate gene expression for floral initiation and development in crested wheatgrass. Three cDNA libraries were generated and sequenced to represent three successive growth stages by sampling leaves at the stem elongation stage, spikes at boot and anthesis stages. The sequencing generated 25,568,846; 25,144,688 and 25,714,194 qualified Illumina reads for the three successive stages, respectively. De novo assembly of all the reads generated 311,671 transcripts with a mean length of 487 bp, and 152,849 genes with an average sequence length of 669 bp. A total of 48,574 (31.8%) and 105,222 (68.8%) genes were annotated in the Swiss-Prot and NCBI non-redundant (nr) protein databases, respectively. Based on the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database, 9,723 annotated sequences were mapped onto 298 pathways, including plant circadian clock pathway. Specifically, 113 flowering time-associated genes, 123 MADS-box genes and 22 CONSTANS-LIKE (COL) genes were identified. A COL homolog DN52048-c0-g4 which was clustered with the flowering time genes AtCO and OsHd1 in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.), respectively, showed specific expression in leaves and could be a CONSTANS (CO) candidate gene. Taken together, this study has generated a new set of genomic resources for identifying and characterizing genes and pathways involved in floral transition and development in crested wheatgrass. These findings are significant for further understanding of the molecular basis for late maturity in this grass species.

Characterization of Oncidium 'Gower Ramsey' transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time

Oncidium 'Gower Ramsey' is a valuable and successful commercial orchid for the floriculture industry in Taiwan. However, no genome reference for entire sequences of the transcribed genes currently exists for Oncidium orchids, to facilitate the development of molecular biological studies and the breeding of these orchids. In this study, we generated Oncidium cDNA libraries for six different organs: leaves, pseudobulbs, young inflorescences, inflorescences, flower buds and mature flowers. We utilized 454-pyrosequencing technology to perform high-throughput deep sequencing of the Oncidium transcriptome, yielding >0.9 million reads with an average length of 328 bp, for a total of 301 million bases. De novo assembly of the sequences yielded 50,908 contig sequences with an average length of 493 bp from 796,463 reads and 120,219 singletons. The assembled sequences were annotated using BLAST, and a total of 12,757 and 13,931 unigene transcripts from the Arabidopsis and rice genomes were matched by TBLASTX, respectively. A Gene Ontology (GO) analysis of the annotated Oncidium contigs revealed that the majority of sequenced genes were associated with 'unknown molecular function', 'cellular process' and 'intracellular components'. Furthermore, a complete flowering-associated expressed sequence that included most of the genes in the photoperiod pathway and the 15 CONSTANS-LIKE (COL) homologs with the conserved CCT domain was obtained in this collection. These data revealed that the Oncidium expressed sequence tag (EST) database generated in this study has sufficient coverage to be used as a tool to investigate the flowering pathway and various other biological pathways in orchids. An OncidiumOrchidGenomeBase (OOGB) website has been constructed and is publicly available online (http://predictor.nchu.edu.tw/oogb/).

From leaf to flower: revisiting Goethe's concepts on the ¨metamorphosis¨ of plants

Goethe’s seminal scientific work, Versuch die Metamorphose der Pflanzen zu erklaren (An Attempt to Interpret the Metamorphosis of Plants) dated from 1790, has created the foundations for many domains of modern plant biology. The archetypal leaf concept, which considers floral organs as modified leaves, besides being the best known has been proven true, following the description of the ABC molecular model of floral organ identity determination during the last decade. Here we analyze the whole theoretical frame of Goethe’s 1790 publication and present two previously misconsidered aspects of this work: The "refinement of the sap" concept as a directional principle and the "cycles of contractions and expansions" as cycles of differential determination of the shoot apical meristem. The reinterpretation of these concepts are in line with the modern view that molecular networks integrate both environmental and endogenous cues and regulate plant development. This reassessment also helps to elaborate a theoretical frame that considers the evolutionary conservation of the molecular mechanisms that regulate plant development.