PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

Abstract

The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

“…The study of core plant genes combined with expression states provides a simple means to enlarge our understanding of the evolution of gene function versus regulation. From the 8,478 conserved Arabidopsis core genes (with homologs in all nine plant species present in the PLAZA comparative genomics platform; Proost et al, 2009), 1,787 genes were present in 1:1 orthologous families. Of these core genes, 80% (1,426 of 1,787) had conserved ECC patterns, revealing a 3% increase in conserved coexpression state compared with the average level in the complete data set (P , 8.5e-05; hypergeometric distribution).…”

“…Inparalogs are gene duplicates postdating speciation. Recent benchmark studies have shown that the OrthoMCL gene-clustering method performs well in modeling recent and ancient duplication events compared with more advanced methods based on phylogenetic inference Proost et al, 2009). For every functional category (see below), all genes with one or more orthologous gene in the other species were retained for the EC analysis.…”

“…From this alignment, unambiguously aligned positions were retained for further analysis (Proost et al, 2009). Synonymous and nonsynonymous substitutions (Ks and Ka) were estimated with codeml (part of the PAML package; Yang, 1997) with the following parameter settings: verbose 0, noisy 0, runmode 22, seqtype 1, model 0, NSsites 0, icode 0, fix_alpha 0, fix_kappa 0, and RateAncestor 0.…”

“…MAPMAN results are reported in Supplemental Table S8. Colinear regions between Arabidopsis and rice were computed with i-ADHoRe and retrieved from PLAZA, a comparative genomics resource (Proost et al, 2009). …”

Arabidopsis Lunapark proteins are involved in ER cisternae formation

“…Genes orthologous to LNP1 and LNP2 in other species within the land plant lineage (Embryophyta) and containing the InterPro LNP domain (IPR019273) were identified using the P laza 4.0 online platform (Proost et al ., 2009). This resulted in the identification of 87 LNP‐like genes from 49 plant species.…”