Guerrero-Sanchez, V. M. | bioRxiv Science

bioRxiv2025

Integrative multi-layer workflow for quantitative analysis of post-translational modifications

Novel algorithms based on ultratolerant database searching have paved the way for comprehensive analysis of all possible post-translational modifications (PTM) that can be detected by mass spectrometry-based proteomics, obviating their prior knowledge. These tools together with novel quantitative statistical models allow hypothesis-free approaches to study the role and impact of PTM on biological systems. However, interpretation of this information from a pathophysiological perspective is challenging due to the huge amounts of PTM data, the existence of chemical, structural, and statistical artifacts and the lack of dedicated tools for their analysis. Here we propose a novel integrative workflow that automatically captures several layers of PTM-related information, including variations in trypsin efficiency, zonal changes, specific PTM changes and hypermodified regions, allowing advanced control of artefacts and coherent and comprehensive interpretation of PTM data. We show the performance of the new workflow by reanalyzing proteomics data from animal models of mitochondrial heteroplasmy and ischemia/reperfusion, revealing relevant PTM information not previously detectable, including consistent detection of novel oxidative modifications in Met and Cys residues from raw proteomics data. The workflow is available through the application PTM-compass.

bioinformatics↗

bioRxiv2022

A first draft genome of Holm oak (Quercus ilex L.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem dehesa

The holm oak (Quercus ilex L.) is the most representative species of the Mediterranean Basin and the agrosilvopastoral Spanish "dehesa" ecosystem. Being part of our life, culture, and subsistence since ancient times, it has great environmental and economic importance. More recently, there has been a renewed interest in using the Q. ilex acorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying on the short and medium term. Breeding programs informed by selection of elite genotypes seems to be the only plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality Q. ilex reference genome. Here, we introduce the first draft genome assembly of Q. ilex using long-read sequencing (PacBio). The assembled nuclear haploid genome has 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) are repetitive sequences. We annotated 39,443 protein-coding genes and Benchmarking Universal Single-Copy Orthologs analysis detected 412 out of 425 expected complete and single-copy genes (94.80%) within the Q. ilex genome. The chloroplast genome size was 142.3 Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of - omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated to resilience against oak decline syndrome and climate change, higher acorn productivity and nutraceutical value.

genomics↗