ARCADE (ARChaeplastida Annotation DatabasE): um banco de dados para estudos genômicos comparativos sobre a evolução de fenótipos complexos em Archaeplastida

Abstract

The abundance of plant genomic data as a result of decreasing sequencing costs contrasts with the lack of databases that integrate these data with genomic annotation, taxonomy and phenotypes to produce statistically solid and biologically relevant knowledge. Here we present ARCADE (ARChaeplastida Annotation DatabaseE), a database of 171 high quality non-redundant Archaeplastida proteomes collected from six different primary sources, along with proteome quality metrics and an increasing number of associated metadata. As case studies to demonstrate the usefulness of ARCADE, we investigated three contrasting evolutionary scenarios in phylogenetic and phenotypic terms: 1) the expansion and contraction of protein domains associated with genome size (GS) evolution in land plants; 2) the evolution of maximum height in angiosperms; 3) and the origin and evolution of the DELAY OF GERMINATION1 gene family (DELAY OF GERMINATION1 Gene Family, DGF) in Archaeplastida. We integrated the genomic annotations and phylogenetic information available in ARCADE together with publicly available phenotypic data to investigate two complex and highly variable plant phenotypes (GS and height). GS appears to be decreasing throughout evolution, except for a few branches that may have undergone independent GS increases. We found that GS variation in land plants is mainly related to nucleotide metabolism, DNA repair, and genome organization. We also saw that in larger genomes there is a higher frequency of the histone 2A superfamily, responsible for several functions, including the formation of nucleosomes and silencing of transposable elements (though epigenetic modifications). Our results indicate that there may be an association between genome size variation in land plants and the preservation of genome stability, suggesting the evolution of mechanisms to help land plants deal with GS variation. Regarding the evolution of height in angiosperms, we highlight the detection of independent expansions of the self-incompatibility system in taller angiosperms, a molecular mechanism that reduces inbreeding and increases genetic diversity. Taller angiosperms have lower evolutionary rates, as they also have longer life cycles than smaller plants, usually annuals. The expansion of self-incompatibility systems in taller angiosperms may be an important factor causing an increase in genetic variability in these species, counterbalancing their lower evolutionary rates. The DGF is a key component in the regulation of many processes in angiosperms, such as germination and flowering. However, it can be found in non-angiosperm land plants. Our search in 171 species of the main Archaeplastida clades detected the presence of genes of this family in 6 species of Charophyta. This result is evidence of an older origin for this gene family than previously thought and contributes to the discussion of the evolution of DGFs. Taken together, the results we obtained from these case studies demonstrate the innovation and scientific relevance of ARCADE, a resource for comparative genomic studies of the evolution of complex phenotypes in plants.