Aureliano Bombarely

Instituto de Biología Molecular y Celular de Plantas (IBMCP) | IBMCP · Department of Biotechnology

Recently diverged species may hybridize in their contact zones if complete reproductive isolation has not yet emerged. Petunia inflata and P. interior are closely related species with a narrow geographic distribution in Argentina and southern Brazil. They share morphological features, genetic markers, pollinators, and occupy a transitional area bet...

Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation‐by‐distance (IBD), isolation‐by‐adaptation (IBA), and isolation‐by‐colonization (IBC) have been recognized as the main divergence pat...

Avocado is an important agricultural food crop in many countries worldwide. Phytophthora cinnamomi, a hemibiotrophic oomycete, remains one of the most devastating pathogens within the avocado industry, as it is near impossible to eradicate from areas where the pathogen is present. A key aspect to Phytophthora root rot disease management is the use...

Gene expression manipulation of specific metabolic pathways can be used to obtain bioaccumulation of valuable molecules and desired quality traits in plants. A single-gene approach to impact different traits would be greatly desirable in agrospace applications, where several aspects of plant physiology can be affected, influencing growth. In this w...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Aim Pleistocene climate oscillations influenced the species distribution and genetic diversity in grasslands, and such climatic changes promoted expansion and contraction cycles, leading to fragmentation and isolation of evolutionary lineages in refuges. This study aimed to infer the evolutionary processes that most influenced the genetic diversity...

Transposable elements (TE) are a major force in the production of new alleles during domestication, nevertheless their use for association studies has been limited due to their complexity. We have developed a TE genotyping pipeline (TEMarker) and apply to 176 Oryza sativa cv japonica whole genome sequence GWAS data in order to identify genetic elem...

Citation: Friel, J.; Bombarely, A.; Fornell, C.D.; Luque, F.; Fernández-Ocaña, A.M. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.. Plants Abstract: Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediter-ranean basin. Thousands of cul...

The olive tree of Vouves in Crete, is considered the oldest producing olive tree in the world with an estimated age exceeding 4000 years. In the present study, we sequenced two samples (from the bottom and the top of the tree) to elucidate the genetic relation of this ancient tree with other olive cvs as well as to gain some insights about its orig...

Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in s...

Vascular wilt, caused by the pathogen Fusarium oxysporum f. sp. physali ( Foph ), is a major disease of cape gooseberry ( Physalis peruviana L.) in Andean countries. Despite the economic losses caused by this disease, there are few studies related to molecular mechanisms in the P. peruviana — Foph pathosystem as a useful tool for crop improvement....

Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit...

Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in sp...

K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. As the first examples, K-seq in species as diverse as...

Hybridization between closely related plant species is a widespread phenomenon with significant evolutionary consequences, so natural hybrid zones provide exciting opportunities to study the processes of genetic differentiation and species formation. In Petunia, genetics, ecology and evolution of pollination syndromes have been thoroughly studied a...

The plant hormone auxin is a fundamental regulator of organ patterning and development that regulates gene expression via the canonical AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) combinatorial system. ARF and Aux/IAA factors interact, but at high auxin concentrations, the Aux/IAA transcriptional repressor is degraded, allo...

Background: Transposable elements (TEs) constitute the vast majority of all eukaryotic DNA, and display extreme diversity, with thousands of families. Given their abundance and diversity, TEs discovery and annotation becomes challengeable. At present, tools and databases have built libraries to mask TEs in genomes based on de novo- and homology-bas...

Motivation: Transposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis. Results: We developed a novel tool, DeepTE, which cl...

The primary domestication of olive (Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000–5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes whic...

Nicotiana benthamiana originates from northern Australia and belongs to the Suaveolentes section. It is used extensively as a model organism for many types of research, including plant–pathogen interactions, RNA interference, and functional genomics. Recent publications that used N. benthamiana as a model for plant–pathogen interactions focused mai...

Motivation Transposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis. Results We developed a novel tool, DeepTE, which classi...

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popula...

Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic divers...

Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resis...

Domesticated plants are essential for agriculture and human societies. Hence, understanding the processes of domestication will be crucial as we strive for more efficient crops and improvements to plants that benefit humankind in other ways. Here, we study the ornamental plant Sinningia speciosa, and reveal that despite the incredible variety found...

Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploi...

Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84‐Gb chromosome‐scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb, and a super‐scaffold N50 of 252.52 Mb, which is the first chromosome‐scale assembled genome of a cool‐se...

Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops,...

The commercial release of third-generation sequencing technologies (TGSTs), giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprec- edented accuracy across complex repeat regions. We survey here a wide range of emerging sequencing platforms and analytica...

A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists was beginning to be appreciated. Scientists were using it to study plant-microbe and protein-protein interactions, and it was the species of choice with which to activate plasmid-encoded viruses, screen for gene functions with virus-induced gene silencing (VIG...

Background Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly h...

The publication of two high-quality rose reference genomes opens new possibilities for a better understanding of the rise of the phenotypic diversity behind domestication.

Phenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, cross-over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed r...

Figure S2 Distribution of N50 for contigs (A) and scaffolds (B) for different k‐mer size values.

Figure S4 Summary of the structural annotation of C. pepo genome.

Table S3 Scaffolds of genome assembly v.3.2. containing chloroplastic and mitochondrial regions. The pseudochromosomes were built from the version 3.2 scaffolds.

Table S8 List of genes that are duplicated in Cucurbita pepo. Predicted functions are also shown.

Figure S5 Transcriptome GO annotation statistics A) by levels and B) at level 6.

Figure S6 Genome GO annotation statistics (A) by levels and (B) at level 6.

Table S1 Accessions of domesticated and wild Cucurbita spp. used for transcriptomic and phylogenetic analyses. The number of reads used for assembly the transcriptomes, and number of genes and transcripts obtained are also shown.

Table S2 NGS library statistics. Numbers of raw reads, percentage of nucleotides over 30 quality, coverage, % of reads filtered out during the cleaning process, % of reads without adaptor, % of chimeric reads, number of cleaned reads, coverage of cleaned reads, and percentage of nucleotides over 30 quality in the clean reads.