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Dissecting plant genomes with the PLAZA comparative genomics platform

(2012) PLANT PHYSIOLOGY. 158(2). p.590-600
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
Keywords
ANNOTATION, TREE, ALGORITHM, ARABIDOPSIS, EUKARYOTIC GENOMES, PROTEIN FAMILIES, GENE ONTOLOGY, SEQUENCE, DRAFT GENOME, EVOLUTION

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Citation

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Chicago
Van Bel, Michiel, Sebastian Proost, Elisabeth Wischnitzki, Sara Movahedi, Christopher Scheerlinck, Yves Van de Peer, and Klaas Vandepoele. 2012. “Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform.” Plant Physiology 158 (2): 590–600.
APA
Van Bel, M., Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y., & Vandepoele, K. (2012). Dissecting plant genomes with the PLAZA comparative genomics platform. PLANT PHYSIOLOGY, 158(2), 590–600.
Vancouver
1.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, et al. Dissecting plant genomes with the PLAZA comparative genomics platform. PLANT PHYSIOLOGY. 2012;158(2):590–600.
MLA
Van Bel, Michiel, Sebastian Proost, Elisabeth Wischnitzki, et al. “Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform.” PLANT PHYSIOLOGY 158.2 (2012): 590–600. Print.
@article{2090381,
  abstract     = {With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.},
  author       = {Van Bel, Michiel and Proost, Sebastian and Wischnitzki, Elisabeth and Movahedi, Sara and Scheerlinck, Christopher and Van de Peer, Yves and Vandepoele, Klaas},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keyword      = {ANNOTATION,TREE,ALGORITHM,ARABIDOPSIS,EUKARYOTIC GENOMES,PROTEIN FAMILIES,GENE ONTOLOGY,SEQUENCE,DRAFT GENOME,EVOLUTION},
  language     = {eng},
  number       = {2},
  pages        = {590--600},
  title        = {Dissecting plant genomes with the PLAZA comparative genomics platform},
  url          = {http://dx.doi.org/10.1104/pp.111.189514},
  volume       = {158},
  year         = {2012},
}

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