Coffea Genome Evolution (EvoGeC)
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Institut de Recherche pour le Développement (IRD), UMR DIADE, Montpellier, Department of Electronics and Automation, Universidad Autónoma de Manizales, Colombia
IRD
UMR DIADE
911 Ave Agropolis
34000 Montpellier
Scientific Interest
Transposable elements and more particularly LTR retrotransposons represent the vast majority of plant genome sequences. They contribute to the variation in chromosome structure and genome size. They also have the potential to alter gene expression and have a significant impact on the phenotypic and genetic diversity of species. The genus Coffea is composed of 124 species, including cultivated species of Arabica (C. arabica) and Robusta (C. canephora). Genome sizes range from 420 Mb to 900 Mb depending on geographical gradients in Africa and Madagascar, suggesting that variation in repeated sequences may be involved in the process of evolution and speciation. A recent assessment has indicated that 60% of wild species are now threatened with extinction, which reinforces the urgency to conserved and analyze them. Our group is studying the mechanisms of evolution of the genome of the genus Coffea using genomic and bioinformatic approaches through massive sequencing of species of the genus, using long and short reading technologies. We are particularly interested in understanding the mechanism of variation in genome size within the genus and its consequences on genome structure and species adaptation. At the intraspecific level, the impact of transposable elements on the phenotypic and genetic diversity of species is studied through the analysis of re-sequencing data. To achieve these objectives, bioinformatic tools are being developed to detect insertion polymorphisms and to detect and annotate LTR retrotransposon at the lineage level in genomic data using artificial intelligence. Understanding the mechanisms of genome size variation and its consequences in Coffea species will improve our knowledge of the evolution of the genus.
Transposable elements and more particularly LTR retrotransposons represent the vast majority of plant genome sequences. They contribute to the variation in chromosome structure and genome size. They also have the potential to alter gene expression and have a significant impact on the phenotypic and genetic diversity of species. The genus Coffea is composed of 124 species, including cultivated species of Arabica (C. arabica) and Robusta (C. canephora). Genome sizes range from 420 Mb to 900 Mb depending on geographical gradients in Africa and Madagascar, suggesting that variation in repeated sequences may be involved in the process of evolution and speciation. A recent assessment has indicated that 60% of wild species are now threatened with extinction, which reinforces the urgency to conserved and analyze them. Our group is studying the mechanisms of evolution of the genome of the genus Coffea using genomic and bioinformatic approaches through massive sequencing of species of the genus, using long and short reading technologies. We are particularly interested in understanding the mechanism of variation in genome size within the genus and its consequences on genome structure and species adaptation. At the intraspecific level, the impact of transposable elements on the phenotypic and genetic diversity of species is studied through the analysis of re-sequencing data. To achieve these objectives, bioinformatic tools are being developed to detect insertion polymorphisms and to detect and annotate LTR retrotransposon at the lineage level in genomic data using artificial intelligence. Understanding the mechanisms of genome size variation and its consequences in Coffea species will improve our knowledge of the evolution of the genus.
Database
| Name | Link |
|---|---|
| Material Design Color Palette | GitHub |
| Material Design Iconic Font | Codepen |
Bioinfo Tools
[{"name": "NGSEP TF: Efficient homology-based annotation of transposable elements using minimizers","url":"https://doi.org/10.1002/aps3.11520"},{"name":"Inpactor2 LTR retrotransposon detector and classificator using Deep Learning","url":"https://github.com/simonorozcoarias/Inpactor2"},{"name": "TIP_Finder An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets","url":"https://github.com/simonorozcoarias/TIP_finder"}]
| Name | Link |
|---|---|
| Material Design Color Palette | GitHub |
| Material Design Iconic Font | Codepen |
Thematic