Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.

Background: Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.

Genome mining of metabolic gene clusters in the Rubiaceae family.

The Rubiaceae plant family, comprising 3 subfamilies and over 13,000 species, is known for producing significant bioactive compounds such as caffeine and monoterpene indole alkaloids. Despite an increase in available genomes from the Rubiaceae family over the past decade, a systematic analysis of the metabolic gene clusters (MGCs) encoded by these genomes has been lacking. In this study, we aim to identify and analyze metabolic gene clusters within complete Rubiaceae genomes through a comparative analysis of eight species.

Genome-Wide Analysis of Lipoxygenase (LOX) Genes in Angiosperms.

Lipoxygenases (LOXs) are enzymes that catalyze the addition of an oxygen molecule to unsaturated fatty acids, thus forming hydroperoxides. In plants, these enzymes are encoded by a multigene family found in several organs with varying activity patterns, by which they are classified as LOX9 or LOX13. They are involved in several physiological functions, such as growth, fruit development, and plant defense.

Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.

Analysis of differential gene expression from RNA-seq data has become a standard for several research areas. The steps for the computational analysis include many data types and file formats, and a wide variety of computational tools that can be applied alone or together as pipelines. This paper presents a review of the differential expression analysis pipeline, addressing its steps and the respective objectives, the principal methods available in each step, and their properties, therefore introducing an organized overview to this context.

Genome-wide association study for resistance to pv. in .

Bacteria halo blight (BHB), a coffee plant disease caused by pv. , has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most cultivars are susceptible to this disease.

Comparative analyses of Theobroma cacao and T. grandiflorum mitogenomes reveal conserved gene content embedded within complex and plastic structures.

Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known species in Theobroma L.

Physiological and Molecular Responses of Woody Plants Exposed to Future Atmospheric CO Levels under Abiotic Stresses.

Climate change is mainly driven by the accumulation of carbon dioxide (CO) in the atmosphere in the last century. Plant growth is constantly challenged by environmental fluctuations including heat waves, severe drought and salinity, along with ozone accumulation in the atmosphere. Food security is at risk in an increasing world population, and it is necessary to face the current and the expected effects of global warming.

A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja.

Terpenoids are a class of compounds that are found in all living organisms. In plants, some terpenoids are part of primary metabolism, but most terpenes found in plants are classified as specialized metabolites, encoded by terpene synthases (TPS). It is not obvious how to assign the putative product of a given TPS using bioinformatics tools.

An Atlas of Plant Transposable Elements.

Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements (TEs) are common characteristics of many genomes. TEs are ubiquitous and dispersed repetitive DNA sequences that frequently impact the evolution and composition of the genome, mainly due to their redundancy and rearrangements.

MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors.

One of the main challenges in applying machine learning algorithms to biological sequence data is how to numerically represent a sequence in a numeric input vector. Feature extraction techniques capable of extracting numerical information from biological sequences have been reported in the literature. However, many of these techniques are not available in existing packages, such as mathematical descriptors.

Computational Analysis of Transposable Elements and CircRNAs in Plants.

This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features.

TERL: classification of transposable elements by convolutional neural networks.

Transposable elements (TEs) are the most represented sequences occurring in eukaryotic genomes. Few methods provide the classification of these sequences into deeper levels, such as superfamily level, which could provide useful and detailed information about these sequences. Most methods that classify TE sequences use handcrafted features such as k-mers and homology-based search, which could be inefficient for classifying non-homologous sequences.

Feature extraction approaches for biological sequences: a comparative study of mathematical features.

As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems, the results are largely affected by the type and number of features extracted. This effect has motivated new algorithms and pipeline proposals, mainly involving feature extraction problems, in which extracting significant discriminatory information from a biological set is challenging.

Genome-Wide Screening and Characterization of Non-Coding RNAs in .

grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the genome.

Low-Copy Genes in Terpenoid Metabolism: The Evolution and Expression of and Genes in Angiosperms.

Terpenoids are a diverse class of metabolites that impact plant metabolism in response to environmental cues. They are synthesized either via a predominantly cytosolic (MVA) pathway or a plastidic pathway (MEP). In , several enzymes from the MVA and MEP pathways are encoded by gene families, excluding and , which are single-copy genes.

Transcriptional patterns of L. nitrate reductase, glutamine and asparagine synthetase genes are modulated under nitrogen suppression and coffee leaf rust.

This study evaluated the transcriptional profile of genes related to nitrogen (N) assimilation in coffee plants susceptible and resistant to rust fungi under N sufficiency and N suppression. For this purpose, we inoculated young coffee leaves with uredospores and collected them at 0, 12, 24 and 48 hours post-inoculation (HPI) to evaluate the relative expressions of genes encoding cytosolic ( ), plastid ( ), (), and (). The genes exhibited distinct patterns of transcriptional modulation for the different genotypes and N nutritional regimes.

Low root PIP1-1 and PIP2 aquaporins expression could be related to reduced hydration in 'Rangpur' lime plants exposed to aluminium.

In acidic soils, aluminium (Al) occurs as Al3+, which is phytotoxic. One of the most conspicuous symptoms of Al toxicity is the root growth inhibition, which can lead to low water uptake and consequent reduction in leaf hydration and gas exchange. However, fibrous xylem vessels have been observed in roots of 'Rangpur' lime plants (Citrus limonia L.

The Terrestrial Carnivorous Plant Sheds Light on Environmental and Life-Form Genome Plasticity.

belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of , we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort (2 = 40, 1C = 317.

Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers.

Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard's coefficient and population structure in 33 genotypes of C.

Decarboxylation mechanisms of C4 photosynthesis in Saccharum spp.: increased PEPCK activity under water-limiting conditions.

Background: C4 plants have been classified into three subtypes based on the enzymes used to decarboxylate C4 acids in the bundle sheath cells (NADP-ME, NAD-ME and PEPCK pathways). Evidences indicate that, depending on environmental factors, C4 plants may exhibit a certain degree of flexibility in the use of the decarboxylation mechanisms. In this context, the objective was to extend the knowledge on the degree of flexibility between the pathways of decarboxylation in sugarcane, a NADP-ME species, at different levels of water deficit.

mirtronDB: a mirtron knowledge base.

Motivation: Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops.