Biology subjects

Almeida, J. V. d. A.

Publications and source records attributed to Almeida, J. V. d. A..

2 recordsLinked to original sources

bioRxiv2026

Comparative Genomics of COBRA-like Genes in Theobroma and Herrania Reveals Structural Conservation and Lineage-Specific Variation

COBRA-like (COBL) genes encode plant-specific proteins associated with cell-wall organization, cellulose deposition, and developmental processes. Despite their functional relevance in model plants and crops, this gene family remains poorly characterized in Amazonian Malvaceae species. Here, we performed a comparative genomic analysis of COBL genes in two Theobroma grandiflorum clones, two T. cacao cultivars, and Herrania umbratica. Using homology searches, conserved domain validation, phylogenetic reconstruction, gene structure analysis, chromosomal mapping, transcript abundance profiling, molecular modeling, and selection tests, we identified 62 COBL genes across the analyzed genomes. COBL copy number varied among genomes, with T. cacao Matina showing the largest repertoire. All retained proteins contained the conserved COBRA domain and grouped into the two major COBL subgroups previously described in angiosperms, with subgroup-specific exon-intron organization largely conserved across species. Genomic distribution and duplication classification indicated contributions from tandem, segmental, dispersed, and proximal duplications, suggesting that multiple genomic processes shaped COBL family organization in Theobroma and Herrania. Phylogenetic analyses further recovered a putative lineage-specific COBL clade within the analyzed Malvaceae, indicating lineage-specific variation in this gene family. Structural modeling indicated overall conservation between representative proteins from this clade and COBL6-associated proteins, although localized amino acid differences were observed within the COBRA domain. Selection analyses supported predominant purifying selection across the family, with limited evidence of episodic diversifying selection in specific lineages and no significant branch-level signal within the putative lineage-specific clade after correction. Overall, these results provide a comparative framework for COBL gene evolution in Theobroma and Herrania and identify candidate genes for future functional studies on cell-wall-related traits in economically important Malvaceae crops.

bioinformatics↗

bioRxiv2022

Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants

The abundance of plant genomic information caused by the decrease of sequencing costs contrasts with the lack of databases that integrate genome annotation, taxonomy and phenotypes to produce statistically sound, biologically meaningful knowledge. Here we present ARCADE (ARChaeplastida Annotation DatabasE), a database of 171 high-quality archaeplastidian non-redundant proteomes gathered from six primary genomic databases, together with proteome quality metrics anda growing number of associated metadata. As a case study to demonstrate the usefulness of ARCADE, we used it to investigate the expansion and contraction of protein domains associated with the evolution of genome size (hereafter GS). GS varies greatly among land plants and the synthesis of large genomes can be costly to cells. Although GS has been studied extensively for decades, the molecular mechanisms involved in the adaptations of plants to the increase in GS are still poorly understood. We used the annotation and phylogenetic information available in ARCADE, together with estimated GS values available for 83 land plant species, to search for associations between the abundance of protein domain families in these species and GS variation through phylogenetic-aware methods. Additionally, we estimated the GS for the ancestral nodes of the extant land plant species. GS seems to be decreasing along the course of evolution, except for a few branches that might have undergone independent GS increases. We found 7 Pfam correlated with the variation in GS in land plants, mainly related to nucleotide metabolism, DNA repair and genome organization. We found larger genomes to have a greater frequency of the Histone 2A superfamily, responsible for diverse functions, including the nucleosome formation and silencing of transposable elements. These molecular functions we found correlated to GS variation suggests they may be associated with preserving genome stability in larger genomes, and might indicate the evolution of mechanisms to cope with the variation in GS in land plants. ARCADE is available at https://bit.ly/ARCADE_OSF.

plant biology↗