Unai Lopez de Heredia

Unai Lopez de Heredia
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Unai verified their affiliation via an institutional email.
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Unai verified their affiliation via an institutional email.
Universidad Politécnica de Madrid | UPM · Departamento de Sistemas y Recursos Naturales

PhD in Forestry, Master in Bioinformatics

About

111
Publications
65,985
Reads
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1,408
Citations
Introduction
I am PhD in Forestry (Forest Genetics) and Master in Bioinformatics. I teach Plant Anatomy and Biology. My research is focused on the adaptability of forest tree species to environmental factors combining anatomical, physiological and genetic approaches. Currently I am involved in the development of bioinformatic pipelines to analyze NGS data (RNA-seq, RADs) in Mediterranean pine and oak species.
Additional affiliations
January 2004 - April 2024
Universidad Politécnica de Madrid
Position
  • Profesor Titular de Universidad
Description
  • Currently I'm working on hybridization in Mediterranean evergreen oaks and on developing bioinformatics solutions especially optimized for forest tree species -omics
January 2001 - November 2005
Universidad Politécnica de Madrid
Position
  • Becario pre-doctoral
Education
October 2013 - October 2014
ENS-ISCIII
Field of study
  • Bioinformatics and Computational Biology
January 2002 - November 2006
Universidad Politécnica de Madrid
Field of study
  • Forest Genetics
September 1995 - July 2001
University of Valladolid
Field of study
  • Forestry

Publications

Publications (111)
Article
Double digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particul...
Article
Full-text available
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain t...
Article
The increase of sequencing capacity provided by high‐throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non‐model organisms. Subsequent genomic analysis and gene discovery in next‐generation sequencing experiments are, however, bottlenecked by functional annotation. One co...
Article
Full-text available
Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next ge...
Article
Current methodologies of genome‐wide single‐nucleotide polymorphism (SNP) genotyping produce large amounts of missing data that may affect statistical inference and bias the outcome of experiments. Genotype imputation is routinely used in well‐studied species to buffer the impact in downstream analysis, and several algorithms are available to fill...
Article
SimHyb2 simulates the evolution of a fix-sized population with up to 2 genetic pools (species, varieties, et.) under user-defined demographic, reproductive and adaptive scenarios. SH2 provides completely traceable pedigrees of virtual individuals, characterized by a genotype with up to 1,000 independent, neutral nuclear loci. Outputs are easily ada...
Article
The study of growth of woody species is a challenging issue, primarily due to the complexity of the involved processes, which span broad spatial and temporal scales. Very often, this latter aspect almost precludes complete experimentation, thereby hindering the comparison between theoretical predictions and real-world observations. Computer simulat...
Article
Full-text available
Background The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the first periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissue...
Preprint
Practical approaches have become a standard in many scientific disciplines, including population genetics. By analyzing properly selected datasets, the students can calculate parameters and draw conclusions about genetic diversity, differentiation and evolution of populations with higher efficiency than if based exclusively on theoretical lessons....
Article
Full-text available
Global change is affecting the frequency and temporal distribution of frost events. We can expect damage caused by low temperatures to increase specially at the upper limit of a species’ elevation range. Here, we assessed how Pinus canariensis two-year old seedlings from different islands and elevations responded differently to chilling and freezin...
Preprint
Current methodologies of genome-wide Single Nucleotide Polymorphism (SNP) genotyping produce large amounts of missing data that may affect statistical inference and bias the outcome of experiments. Genotype imputation is routinely used in well-studied species to buffer the impact in downstream analysis and several algorithms are available to fill i...
Preprint
The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissues, known as rhyti...
Article
Background Non-model species lacking public genomic resources have an extra handicap in bioinformatics that could be assisted by parameter tuning and the use of alternative software. Indeed, for RNA-seq-based gene differential expression analysis, parameter tuning could have a strong impact on the final results that should be evaluated. However, th...
Article
Full-text available
Hybridization and introgression between cork oak (Quercus suber) and holm oak (Q. ilex) have traditionally been reckoned as undesirable processes, since hybrid individuals lack the profitable bark characteristics of cork oak. Nevertheless, a systematic and quantitative description of the bark of these hybrids at the microscopic level, based on a si...
Preprint
RNA sequencing (RNA-seq) is a high throughput sequencing method that has become one the most employed tools in transcriptomics. The implementation of optimal bioinformatic analyses required in RNA-seq experiments may be complicated due to the large amounts of data generated by the sequencing platforms, along with the intrinsic nature of these data...
Preprint
Hybridization and introgression between cork oak ( Quercus suber ) and holm oak ( Q. ilex ) have traditionally been reckoned as undesirable processes, since hybrid individuals lack the profitable bark characteristics of cork oak. Nevertheless, a systematic and quantitative description of the bark of these hybrids at the microscopic level based on a...
Preprint
Full-text available
NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation se...
Article
Background: Bioinformatic software for RNA-seq analysis has high computational requirement in terms of CPU number, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and the complexity of the algorithms employed. Comparative studies about the...
Article
Aim Understanding the drivers of speciation within islands is key to explain the high levels of invertebrate diversification and endemism often observed within islands. Here, we propose an insular topoclimate model for Quaternary diversification (ITQD), and test the general prediction that, within a radially eroded conical island, glacial climate c...
Article
Full-text available
Polymorphism detection in woody plant species is important in phylogenetics and an essential stage in plant breeding programs. Genotyping has benefitted from the development of next-generation sequencing (NGS) techniques. Methodologies based upon single and double-digested DNA sequencing (RADseq and ddRADseq) allow the detection of polymorphisms on...
Article
RNA-seq analysis usually requires large computing infrastructures. NGScloud is a bioinformatic system developed to analyze RNA-seq data using the cloud computing services of Amazon that permit the access to ad hoc computing infrastructure scaled according to the complexity of the experiment, so its costs and times can be optimized. The application...
Article
Full-text available
Cork oak and holm oak share a large part of their natural range, and are known to hybridize in mixed stands. This hybridization is supposed to have played a relevant role in the past history of cork oak. Previous research has reported that F1 hybrids are produced with holm oak acting as pollen recipient, therefore carrying holm oak chloroplast. Add...
Data
Table S3: Differentially expressed genes (DEG) during wood formation in P. canariensis
Data
Table S2: Complete annotation of the transcriptome for xylogenesis in P. canariensis
Data
Table S1: Probes included in the microarray and correspondence to contigs obtained after meta-assembly of libraries
Article
Full-text available
The genus Quercus is known for the occurrence of frequent hybridization events between species. Although this phenomenon is not common among holm oak (Q. ilex) and cork oak (Q. suber), these species can hybridize when they coexist in mixed stands. The result of hybridization is a viable hybrid progeny with very heterogeneous leaf morphology. Litera...
Article
Full-text available
We present SimHyb, a Java-based software for the simulation of mixed hybridizing populations. The software incorporates user-defined initial parameters and input files to account for the initial census size of two species in a closed population, the number of intermediate specific classes, the directional fertility among specific classes, the fitne...
Chapter
Gene flow among closely related species is a not so unusual event, especially in plants. Hybridization and introgression have probably played a relevant role in the evolutionary history of the genus Quercus, for instance in the post-glacial northwards migration of European white oaks. In the same way, hybridization between the Mediterranean sclerop...
Article
Full-text available
A noticeable proportion of low transcribed genes involved in wood formation in conifers may have been missed in previous transcriptomic studies. This could be the case for genes related to less abundant cell types, such as axial parenchyma and resin ducts, and genes related to juvenile wood. In this study, two normalized libraries have been obtaine...
Article
Full-text available
The Canary Island pine Pinus canariensis is the main forest species of the western Canary Islands. The species occupies a wide range of elevations and climates in sharply different habitats, and it is able to withstand devastating perturbations, such as forest fires or volcanic activity. The remarkable ecological amplitude of the Canary Island pine...
Article
Full-text available
Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has allowed a growing number of gene expression studies focused on forest trees in the last 5 years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging, because the massive genome length (~20.1 Gbp for loblolly pine) and the absence o...
Article
Full-text available
Las técnicas de análisis genómico que se basan en la secuenciación masiva han supuesto una revolución en la última década no sólo en biomedicina o agronomía, sino también en el estudio de la diversidad biológica. Las plataformas de secuenciación de segunda y tercera generación que vienen a complementar a la tradicional secuenciación por el método S...
Conference Paper
Full-text available
Nowadays, there is a great amount of genomic and transcriptomic data available about forest species, including ambitious projects looking for complete sequencing and annotation of different gymnosperm genomes. Pinus canariensis is an endemic conifer of the Canary Islands with re-sprouting capability and resilience against fire and mechanical damage...
Article
Full-text available
Aim of the study: Models that combine parentage analysis from molecular data with spatial information of seeds and seedlings provide a framework to describe and identify the factors involved in seed dispersal and recruitment of forest species. In the present study we used a spatially explicit method (the gene shadow model) in order to assess primar...
Thesis
Full-text available
Next Generation DNA/RNA Sequencing studies produce big amount of data that need to be analyzed with proper computation infrastructure that is not always available for all research centers or universities. Expressional analysis derived from RNA sequencing (RNA-seq) of forest trees is particularly challenging, because the massive genome length (~23.2...
Article
Oceanic islands of volcanic origin provide useful templates for the study of evolution because they are subjected to recurrent perturbations that generate steep environmental gradients that may promote adaptation. Here we combine population genetic data from nuclear genes with the analysis of environmental variation and phenotypic data from common...
Article
Full-text available
Background and Aims It is widely accepted that hydraulic failure due to xylem embolism is a key factor contributing to drought-induced mortality in trees. In the present study, an attempt is made to disentangle phenotypic plasticity from genetic variation in hydraulic traits across the entire distribution area of a tree species to detect adaptation...
Article
Spatial discordance between primary and effective dispersal in plant populations indicates that postdispersal processes erase the seed rain signal in recruitment patterns. Five different models were used to test the spatial concordance of the primary and effective dispersal patterns in a European beech (Fagus sylvatica) population from central Spai...
Article
Full-text available
The effect of non-reproductive trees and saplings as a physical barrier to pollen dispersal in wind-pollinated species’ forests has not received enough attention in the literature so far. The neighborhood seedling model was used to fit pollen dispersal models for beech at different stages of gap recolonization and to elucidate the effect of sapling...
Article
Full-text available
Recent phylogeographic studies have elucidated the effects of Pleistocene glaciations and of Pre-Pleistocene events on populations from glacial refuge areas. This study investigates those effects in riparian trees (Populus spp.), whose particular features may convey enhanced resistance to climate fluctuations. We analysed the phylogeographic struct...