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Dissecting plant genomes with the PLAZA comparative genomics platform

Michiel Van Bel UGent, Sebastian Proost UGent, Elisabeth Wischnitzki UGent, Sara Movahedi UGent, Christopher Scheerlinck, Yves Van de Peer UGent and Klaas Vandepoele UGent (2012) PLANT PHYSIOLOGY. 158(2). p.590-600
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ANNOTATION, TREE, ALGORITHM, ARABIDOPSIS, EUKARYOTIC GENOMES, PROTEIN FAMILIES, GENE ONTOLOGY, SEQUENCE, DRAFT GENOME, EVOLUTION
journal title
PLANT PHYSIOLOGY
Plant Physiol.
volume
158
issue
2
pages
590 - 600
Web of Science type
Article
Web of Science id
000300054300005
JCR category
PLANT SCIENCES
JCR impact factor
6.555 (2012)
JCR rank
8/193 (2012)
JCR quartile
1 (2012)
ISSN
0032-0889
DOI
10.1104/pp.111.189514
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2090381
handle
http://hdl.handle.net/1854/LU-2090381
date created
2012-04-18 14:09:27
date last changed
2013-05-06 11:10:07
@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},
}

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.