Examinando por Autor "Meisel, L."
Mostrando 1 - 4 de 4
Resultados por página
Opciones de ordenación
Ítem Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica(BMC, 2013-12) Immanen, J.; Nieminen, K.; Duchens Silva, H.; Rodríguez Rojas, F.; Meisel, L.; Silva, H.; Albert, V.; Hvidsten, T.; Helariutta, Y.Background: Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species.Results: Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses.Conclusions: In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.Ítem Construction and Comparative Analyses of Highly Dense Linkage Maps of Two Sweet Cherry Intra-Specific Progenies of Commercial Cultivars(Public Library of Science, 2013-01) Klagges, C.; Campoy, J.; Quero-García, J.; Guzmán, A.; Mansur, L.; Gratacós, E.; Silva, H.; Rosyara, U.; Lezzoni, A.; Meisel, L.; Dirlewanger, E.Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between 'Black Tartarian' × 'Kordia' (BT×K) and 'Regina' × 'Lapins'(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1-LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.Ítem JUICE: A data management system that facilitates the analysis of large volumes of information in an EST project workflow(BMC, 2006-11) Latorre, M.; Silva, H.; Saba, J.; Guziolowski, C.; Vizoso, P.; Martinez, V.; Maldonado, J.; Morales, A.; Caroca, R.; Cambiazo, V.; Campos-Vargas, R.; Gonzalez, M.; Orellana, A.; Retamales, J.; Meisel, L.Background: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/ Genome projects.Ítem The genome of woodland strawberry (Fragaria vesca)(Springer Nature, 2011) Shulaev, V.; Sargent, D.; Crowhurst, R.; Mockler, T.; Folkerts, O.; Delcher, A.; Jaiswal, P.; Mockaitis, K.; Liston, A.; Mane, Sh.; Burns, P.; Davis, T.; Slovin, J.; Bassil, N.; Hellens, R.; Evans, C.; Harkins, T.; Kodira, Ch.; Desany, B.; Crasta, O.; Jensen, R.; Allan, A.; Michael, T.; Setubal, J.; Celton, J.; Rees, J.; Williams, K.; Holt, S.; Rojas, J.; Chatterjee, M.; Silva, H.; Meisel, L.; Adato, A.; Filichkin, S.; Troggio, M.; Viola, R.; Ashman, T.; Wang, H.; Dharmawardhana, P.; Elser, J.; Raja, R.; Priest, H.; Bryant, D.; Fox, S.; Givan, S.; Wilhelm, L.; Naithani, S.; Christoffels, A.; Salama, D.; Carter, J.; Girona, E.; Zdepski, A.; Wang, W.; Kerstetter, R.; Schwab, W.; Korban, Sh.; Davik, J.; Monfort, A.; Denoyes-Rothan, B.The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria Ã- ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×-39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.