Romain Guyot

Institute of Research for Development | IRD · UMR DIADE

Analysis of eukaryotic genomes requires the detection and classification of transposable elements (TEs), a crucial but complex and time-consuming task. To improve the performance of tools that accomplish these tasks, Machine Learning approaches (ML) that leverage computer resources, such as GPUs (Graphical Processing Unit) and multiple CPU (Central...

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...

LTR retrotransposons (LTR-RT) are major components of plant genomes. These transposable elements participate in the structure and evolution of genes and genomes through their mobility and their copy number amplification. For example, they are commonly used as evolutionary markers in genetic, genomic, and cytogenetic approaches. However, the plant r...

Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in...

The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations c...

Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition and genomic distribution were provided. Here, we exploited the non-codin...

Premise Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and c...

Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease tha...

A common task in bioinformatics is to compare DNA sequences to identify similarities between organisms at the sequence level. An approach to such comparison is the dot-plots, a 2-dimensional graphical representation to analyze DNA or protein alignments. Dot-plots alignment software existed before the sequencing revolution, and now there is an ongoi...

Transposable elements (TEs) are mobile elements found in the majority of eukaryotic genomes. TEs deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In plants, the major group of TEs is Long Terminal Repeats retrotransposons (LTR-RTs). They are classified into superfamilies (Gypsy, Copia) and su...

The domestication process in Lima bean ( Phaseolus lunatus L. ) involves at least two independent events, within the Mesoamerican and Andean gene pools. Both processes produced similar phenotypic changes in landraces, making Lima bean an excellent model to understand convergent evolution. Despite recent research efforts, the mechanisms of adaptatio...

LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification of these elements remains a challenge today. Moreover, current software can be relatively sl...

Climate variability and change are among the major drivers of abiotic stresses and the concomitant vulnerability of agricultural production systems. With the advent of systems biology, the analysis of complex crop-environment interactions through integrated high-throughput approaches, such as genomics, transcriptomics, proteomics, metabolomics, lip...

The group of Baracoffea includes 9 endemic deciduous species which are exclusively present in the dry forests of the West coast of Madagascar. They are particularly well adapted to xerophytic conditions. Deforestation and anthropic activities have caused a strong fragmentation of the Malagasy forests and considerably modified the natural forest eco...

Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes K...

Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caused by a fungal pathogen, Hemileia vastatrix (Hva), belonging to the phylum Basidiomycota. Coffee leaf rust causes significant yield losses and increases costs related to its control, with evaluated losses of USD 1–2 billion annually. It attacks both the...

Transposable elements are mobile sequences that can move and insert themselves into chromosomes, activating under internal or external stimuli, giving the organism the ability to adapt to the environment. Annotating transposable elements in genomic data is currently considered a crucial task to understand key aspects of organisms such as phenotype...

Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Because of their mobility in the host genome, TEs can deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In response to these potential threats, host genomes use various processes to repress the...

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,...

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lych...

Transposable elements are mobile sequences in all eukaryotic genomes. LTR (Long Terminal Repeat) retrotransposons are the most abundant elements in plant genomes where they play a fundamental role in evolution, gene function and genetic diversity. It is therefore important to develop bioinformatic tools to identify them in sequenced genomes and to...

Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements (TEs) are common characteristics of many genomes....

Lagenaria Siceraria, cucurbite consommé en sauce en Côte d'Ivoire La sauce de pistache est très appréciée dans de nombreux pays africains comme la Côte d'Ivoire. La recette est faite à partir de graines de la Cucurbitaceae, Lagenaria siceraria (Molina) Standley. Toutefois chez cette gourde, 2 types se distinguent par leur utilisation. Le type caleb...

Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related...

Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around centromeres. However, proximal regions of Coffea chromosomes remain poorly understood, especially on the nature and organisation of the sequences. Taking advantage of genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabic...

Transposable elements (TEs) are specific structures of the genome of species, which can move from one location to another. For that reason, they can cause mutations or changes that can be negative, such as the appearance of diseases, or beneficial, such as participating in fundamental roles in the evolution of genomes and genetic diversity. Long Te...

Currently, the whole world is facing the problem of global warming, the main cause of which is anthropogenic activity. In Madagascar, deforestation and other anthropogenic activities have caused severe forest fragmentation and have significantly altered natural forest ecosystems. One of the direct consequences is that nearly 75% of Malagasy coffee...

Every day more plant genomes are available in public databases and additional massive sequencing projects (i.e., that aim to sequence thousands of individuals) are formulated and released. Nevertheless, there are not enough automatic tools to analyze this large amount of genomic information. LTR retrotransposons are the most frequent repetitive seq...

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N‐methyltransferase proteins. Here we are reporting on the 422‐Mb chromosome‐level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine‐free, species from the Comoro archipelago. We predicted 32,874 ge...

Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in genome size variation, LTR retrotra...

Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future...

Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future...

Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated charact...

Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. A particular type of TE called LTR-retrotr...

Bottle gourd ( Lagenaria siceraria ) is an important food, medicinal and utilitarian crop with a large pan tropical distribution. The two morphologically different types in the siceraria subspecies are sufficiently different to be considered as varieties but they are assigned into different taxonomic ranks. The genotyping-by-sequencing (GBS) of 95...

For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017—based on 28,800 nuclear SNPs—indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid full-genome sequences highlig...

The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a sc...

Because of the promising results obtained by machine learning (ML) approaches in several fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In genomics, a current issue is to detect and classify transposable elements (TEs) because of the tedious tasks involved in bioinformatics methods. Thus, ML was recentl...

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biolog...

Background and aims: Like other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional, phenological features and reproductive strategies. The trends of interspecific trait variation, which stems fr...

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a...

Background Transposable elements (TEs) constitute the most common repeated sequences in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity, adaptation to the environment and diseases. Although there are many conventional bioinformatics algorithms for detecting and classifying TEs, none have achieved reliable resu...

Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that...

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch). White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi. Nevertheless...

Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to de...

Un alineamiento gráfico o "dot plot" es un método de representación visual del análisis de datos genómicos, comúnmente utilizado para comparar la similitud de dos secuencias biológicas. El programa DOTTER desarrollado en 1995, es la herramienta más utilizada para este tipo de tareas. El mayor problema de este software radica en el elevado tiempo de...

Los retrovirus endógenos humanos (HERVs) constituyen aproximadamente el 8% del genoma humano, particularmente están sobreexpresados en algunas células y tejidos del carcinoma de mama que es el más común y la segunda causa de muerte por cáncer en mujeres en todo el mundo. Investigaciones recientes muestran que la familia de retrovirus HERV-K es la d...

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffe...

Transportable elements (TEs) account for majority of genomic sequences in most plant genomes. They play vital roles in the structure, function, and evolution of genomes. Pineapple (Ananas comosus L.) is an important fruit crop performing CAM photosynthesis and has a relatively small genome size at 526 Mb. But it contains relative high proportion of...

Figure 4. Detailed analysis of four potential cases of horizontal transfer identified in 69 sequenced plant genomes. A. Tree of the 69 plant genomes positioned. Potential cases of horizontal transfer analyzed here are represented by a colored lines connecting species, with the lineage involved, the BLAST score and the nucleotide identity percentage...

Genome editing, which is an unprecedented technological breakthrough, has provided a valuable means of creating targeted mutations in plant genomes. In this study, we developed a genomic web tool to identify all gRNA target sequences in the coffee genome, along with potential off-targets. In all, 8,145,748 CRISPR guides were identified in the draft...

One particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR ret...

LTR-retrotransposons (LTR-RTs) são abundantes nos genomas das plantas, sendo Gypsy e Copia os mais representativos. A região centromérica acumula diferentes arranjos de sequências repetitivas, como DNA satélite e retrotransposons. Neste estudo foram triados LTR-RTs da linhagem CRM, baseado em domínios conservados da gag-POL nos genomas de Coffea ca...

Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in th...

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide as...

Nunca antes se han tenido tantos datos de secuenciación disponibles y la posibilidad de contar con tecnologías que se actualizan constantemente, que permiten estudiar de forma masiva y simultánea cientos de especies para diferentes objetivos, entre los cuales se destacan los estudios de taxonomía molecular, evolución y la producción de compuestos p...