Lorenzo Carretero-Paulet

Universidad de Almería | UAL · Department of Biology and Geology

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide. Cultivated accessions have undergone several population bottlenecks resulting in low genetic diversity. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives o...

Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the...

Background Bud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE ( SVP )-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX ( DAM ), are master regulators of bud dormancy in pe...

The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced and a first draft assembly was published in 2019. Given the extensive uses and culture of moringa, often referred to as the multi...

Citation: Turiel, S.; Garrido-Cardenas, J.A.; Gómez-Serrano, C.; Acién, F.G.; Carretero-Paulet, L.; Blanco, S. A Polyphasic Characterisation of Tetradesmus almeriensis sp. nov. (Chlorophyta: Scenedesmaceae). Abstract: The microalga Tetradesmus almeriensis, previously known as Scenedesmus almeriensis, has been isolated and cultivated as a highly pro...

Abstract It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in...

Post-translational modification by Small Ubiquitin-related Modifier (SUMO) is an essential regulatory mechanism in eukaryotes. In the cell, SUMO conjugates are highly enriched in the nucleus and, consistently, SUMOylation machinery components are mainly nuclear. Nonetheless, cytosolic SUMO targets also exist and the mechanisms that facilitate SUMO...

Whole‐genome duplication (WGD) is a dramatic, common event in plants. Because of the detrimental effects arising from doubling the entire chromosome set, such as minority cytotype exclusion, genomic instability, mitotic and meiotic abnormalities, alterations in cell architecture, or epigenetic changes (Comai, 2005), purifying selection is expected...

The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. a...

The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much resear...

Gene duplicates, generated either through whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechan...

The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. a...

The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research...

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one...

Apicomplexa form a phylum of obligate parasitic protozoa of great clinical and veterinary importance. These parasites synthesize glycoconjugates for their survival and infectivity, but the enzymatic steps required to generate the glycosylation precursors are not completely characterized. In particular, glucosamine-phosphate N-acetyltransferase (GNA...

In several organisms, particular functional categories of genes, such as regulatory and complex-forming genes, are preferentially retained after whole-genome multiplications but rarely duplicate through small-scale duplication, a pattern referred to as reciprocal retention. This peculiar duplication behavior is hypothesized to stem from constraints...

Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental s...

The growing number of genome sequences completed during the last few years has made necessary the development of bioinformatics tools for the easy access and retrieval of sequence data, as well as for downstream comparative genomic analyses. Some of these are implemented as online platforms that integrate genomic data produced by different genome s...

Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly a...

Abscission is the regulated process of detachment of an organ from a plant. In apple the abscission of fruits occurs during their early development to control the fruit load depending on the nutritional state of the plant. In order to control production and obtain fruits with optimal market qualities, the horticultural procedure of thinning is perf...

In plants, CK2α/β subunits are encoded by multigenic families. They assemble as heterotetrameric holoenzymes or remain as individual subunits and are usually located in distinct cell compartments. Here we revise the number of maize CK2α/β genes, bringing them up to a total of eight (four CK2α catalytic and four CK2β regulatory subunits). We charact...

The genome of Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates as many genes a...

Utricularia gibba is an aquatic carnivorous plant with highly specialized morphology, featuring fibrous floating networks of branches and leaf-like organs, no recognizable roots, and bladder traps that capture and digest prey. We recently described the compressed genome of U. gibba as sufficient to control the development and reproduction of a comp...

Orchids have captured imaginations worldwide for hundreds of years. The publication of the moth orchid genome sequence opens the door to a greater understanding of orchid morphological evolution and physiological adaptation.

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanacea...

Biological systems remain robust against certain genetic and environmental challenges. Robustness allows the exploration of ecological adaptations. It is unclear what factors contribute to increasing robustness. Gene duplication has been considered to increase genetic robustness through functional redundancy, accelerating the evolution of novel fun...

Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate if polar bears demonstrate lineage-sp...

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication...

Background To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of retention of duplicate, triplicate, etc. genes. Results We measure the simultaneous dynamics of duplicate orthologous gene loss in...

Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (MEP) pathway. The production of MEP is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (DXR-I) but a few organisms use...

The ubiquitous and conserved cytosolic heat-shock proteins 90 (HSP90A) perform essential functions in the cell. To understand the evolutionary origin of HSP90A functional diversification, we analyzed the distribution of HSP90A family from 54 species representing the main eukaryotic lineages. Three independent HSP90A duplications led to the paralog...

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of th...

Sumoylation is an essential post-translational modification that participates in many biological processes including stress responses. However, little is known about the mechanisms that control SUMO conjugation in vivo. We have evaluated the regulatory role of the heterodimeric E1 activating enzyme, which catalyzes the first step in SUMO conjugatio...

Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be retained than small-scale duplications (SSDs), though their relative contribution to the functional fate o...

Author Summary Gene duplication involves the doubling of a gene, originating an identical gene copy. Early evolutionary theory predicted that, as one gene copy is performing the ancestral function, the other gene copy, devoid from strong selection constraints, could evolve exploring alternative functions. Because of its potential to generate novel...

Genetic interactions and JTT-corrected amino acid divergence of duplicated genes formed by small-scale duplication (SSD) in Saccharomyces cerevisiae. Divergence refers to the distance from a gene copy to the most recent ancestor of the duplication event. Genes are represented by their locus tag in S. cerevisiae. (XLS)

Genetic interactions and JTT-corrected amino acid divergence of duplicated genes formed by whole genome duplication (WGD) in Sacchromyces cerevisiae. Divergence refers to the distance from a gene copy to the most recent ancestor of the duplication event. Genes are named according to their locus tags in S. cerevisiae. (XLS)

Genome sequencing of five Saccharomyces cerevisiae experimentally evolved lines (Msh2_1 to Msh2_5). Characteristics of genomes sequences at different time points of evolution (P20, 30, 50, 70, 90 and a 100) are presented. (XLS)

Sub-cellular localization of duplicated genes in Saccharomyces cerevisiae. Genes are named according to their locus tags in S. cerevisiae, with A referring to one gene copy and B to the other gene copy. (XLS)

Single Nucleotide Polymorphisms (SNPs) fixed during the experimental evolution of five lines (Msh2_1 to Msh2_5) of Saccharomyces cerevisiae. For each of the SNPs we show their exact chromosomal location and position. (XLS)

Gene duplicates are a major source of evolutionary novelties in the form of new or specialized functions and play a key role in speciation. Gene duplicates are generated through whole genome duplications (WGD) or small-scale genome duplications (SSD). Although WGD preserves the stoichiometric relationships between duplicates, those arising from SSD...

Summary of 34 land plant CK2β sequences. Sequence identifier refers to the UNIPROT database, excepting for species examined independently, in which case the accession from the corresponding database was indicated (Table S1). The * designs sequence incomplete at its N-terminal end. Some genes have been identified to encode for alternatively spliced...

Unrooted Maximum Likelihood phylogenetic tree of CK2β regulatory subunits. The tree is based on the CLUSTAL alignment of 69 CK2β protein sequences. The clade clustering land plant CK2β is indicated. Non-land plant CK2β showing N-terminal extensions are in bold. Bootstrap values are displayed next to the corresponding nodes. The tree is drawn to sca...

Unrooted Neighbor Joining phylogenetic tree of CK2β regulatory subunits. The tree is based on the CLUSTAL alignment of 69 CK2β protein sequences. The clade clustering land plant CK2β is indicated. Non-land plant CK2β showing N-terminal extensions are in bold. Bootstrap values are displayed next to the corresponding nodes. The tree is drawn to scale...

Quantification of Rab17 and β-casein phosphorylation with CK2α1/ΔNCK2β1 holoenzyme and increasing amounts of CK2β1 N-terminal domain (1–80). Relative phosphorylation of Rab17 and β-casein with the holoenzyme composed by CK2α1/ΔNCK2β1 with increasing amounts of CK2β1 N-terminal domain (1–80) compared to phosphorylation of both substrates with CK2α1/...