Biology subjects

Sosa, E. J.

Publications and source records attributed to Sosa, E. J..

3 recordsLinked to original sources

bioRxiv2023

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Yerba mate (Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large yerba mate genome size is partly due to a whole-genome duplication (Ip-) during the early evolutionary history of Ilex, in addition to the hexaploidization event ({gamma}) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of its relatives, coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in yerba mate and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the x-ray diffraction data suggests structural constraints are minimal for the convergent evolution of individual reactions.

plant biology↗

bioRxiv2023

Hidden Markov Models based search in combination with structural bioinformatics pipeline leads to the identification of DAF-12 distant orthologous in Meloidogyne incognita

Root-knot nematode (RKN) Meloidogyne spp. is one of the most damaging parasites due to its wide range of hosts. Here, we report a C. elegans receptor DAF-12 ortholog gene in Meloidogyne incognita (DAF-12Minc), a promising molecular target to modify the RKN life cycle. Using a combination of Hidden Markov Models (HMM) based sequence search and phylogenetic analysis we identified three DAF-12Minc genes. Although the global sequence identity between previously reported DAF-12 genes and DAF-12Minc was acceptable, the correlation between binding site residues was low in the multiple sequence alignment (MSA). Since those residues are critical for DAF-12 interaction with its ligand, the dafachronic acids (DAs), and thus its biological role, we investigated whether even if the sequence conservation is low, the active site structure was conserved and thus able to bind DAs. For this purpose, we built accurate homology models of DAF-12Minc and used them to identify and characterize the ligand binding site (LBS) and its molecular interactions with DAs-like compounds. Finally, we cloned, expressed, and evaluated the biological role of DAF-12Minc in vitro and in vivo using a DAF-12 antagonist. These in vivo results suggest that our strategy was effective to find orthologous genes among species even when sequence similarity is low. Author summaryRoot-knot nematodes are parasitic to plants and responsible for causing a significant loss of millions of dollars every year in crops worldwide, which makes it necessary to develop effective strategies to combat them. One popular approach is to identify genes that can serve as molecular targets. Typically, such molecular targets are discovered through basic research on model organisms. However, since they can be quite different from the target organism, conventional tools may not always be efficient in extrapolating results. Dafachronic acids (DAs) are a crucial class of steroid hormones that regulate the development and physiology of nematodes. They are synthesized from cholesterol and are controlled by a nuclear hormone receptor known as DAF-12. This receptor acts as a master regulator of gene expression, playing a vital role in nematode biology, including development, reproduction, metabolism, stress response, and longevity. Therefore, DAF-12 is a promising molecular target for controlling parasitic nematodes. Although DAF-12 was initially discovered in the model organism Caenorhabditis elegans and subsequently found in some parasitic nematodes, previous attempts to identify molecular targets in the Meloidogyne genus failed to detect DAF-12 orthologs. To address this gap, we employed a combination of sequence and structure analysis to identify potential candidates for DAF-12, a known and validated molecular target, which had not yet been found in Meloidogyne incognita. Our bioinformatics predictions were experimentally validated, which may serve as a starting point for future campaigns aimed at developing parasite control strategies based on this relevant molecular target.

bioinformatics↗

bioRxiv2023

De novo assembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Black flounder (Paralichthys orbignyanus) is an economically important ma-rine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina sequencing technology. We started with two independent libraries (from one female and one pool of females; each with 150 bp paired-end reads, a mean insert length of 350 bp, and >35 X-fold coverage). Each library was assembled separately using SOAPdenovo2 and the resulting contigs were scaffolded with SSPACE3 before gaps were filled with GapCloser. In vertebrates, including teleosts, the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to test whether the small genome size of Pleuronectiformes is related to the size of their introns and exons. The assemblies re-sulted in a genome size of [~]538 Mbp (41.35% GC content, 0.11% undetermined bases). Analysis of the assemblies at the core genes level (subset of the 458 universally ex-pressed KOG families) revealed that more than 98% of core genes are present, with more than 78% of them having more than 50% coverage. This indicates a fairly complete and accurate genome at the coding sequence level. Prediction of genes based on statistical predictors (geneid) and sequence-based predictors (Exonerate, using a closely related species, Paralichthys olivaceus, as a reference) was performed. This revealed 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types (including a complete set of spliceosomes and several types of snoRNA and miRNA). As a result, this study concluded that the reduced genome size of flounders is related to a reduction in transcript size, mainly through a reduction in exon number, but also through a reduction in large introns. Thus, both components seem to be involved in the strategy of genome reduction in Pleuronectiformes.

genomics↗