The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes.

The wild species of the Coffea genus present a very wide morphological, genetic, and biochemical diversity. Wild species are recognized more resistant to diseases, pests, and environmental variations than the two species currently cultivated worldwide: C. arabica (Arabica) and C.

Unveiling potential virulence determinants in isolates from through whole genome analyses.

The genus includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on in several marine organisms, no specific studies have been conducted on . This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast.

Efficient homology-based annotation of transposable elements using minimizers.

Premise: Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies.

NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.

Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed.

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans.

Background: The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN).

The genomic study of an environmental isolate of shows its metabolic potential to degrade hydrocarbons.

Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation.

Evolutionary Origins of Rhizarian Parasites.

The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach.

Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.

Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.

Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.