The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Raharimalala, Nathalie; Rombauts, Stéphane; McCarthy, A.A.; Garavito, Andréa; Orozco-Arias, Simón; Bellanger, Laurence; Morales-Correa, Alexa Yadira; Froger, Solène; Michaux, Stéphane; Berry, Victoria; Métairon, Sylviane; Fournier, Coralie; Lepelley, Maud; Mueller, Lukas A.; Couturon, Emmanuel; Hamon, Perla; Rakotomalala, J. J. R.; Descombes, Patrick; Guyot, Romain; Crouzillat, Dominique

doi:10.1038/s41598-021-87419-0

Cited by 30 publications

(16 citation statements)

References 66 publications

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“…However, it is an unprofitable species because its growth in culture is slow, so it is considered an endangered species. C. humblotiana, endemic to the Comoros Archipelago, is a different species from others described within the genus Coffea since it does not produce caffeine; therefore, this species produces a naturally decaffeinated coffee product, and its metabolic pathways are currently under study (Raharimalala et al, 2021).…”

Section: Methodsmentioning

confidence: 99%

Ethnopharmacological study of the genus Coffea and compounds of biological importance

Gallardo-Ignacio

Nicasio-Torres²,

Santibáñez³

et al. 2022

RMIQ

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Section: Methodsmentioning

confidence: 99%

Ethnopharmacological study of the genus Coffea and compounds of biological importance

Gallardo-Ignacio

Nicasio-Torres²,

Santibáñez³

et al. 2022

RMIQ

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“…Once the computational model with the highest F1-Score and accuracy was defined, generalization tests were performed with plant species with different genome sizes such as: Coffea eugenioides (GCA_003713205.1, 678 Mb), Coffea humblotiana (407 Mb) [ 41 ], Oryza indica (GCA_011764405.2, 355 Mb) [ 42 ] and Oryza granulata (GCA_003991445.1, 752 Mb) [ 43 ]. Thus, LTR_STRUC [ 34 ] and LTR_FINDER [ 27 ] software were first run to predict LTR-RTs for each genomes.…”

Section: Methodsmentioning

confidence: 99%

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning

Orozco-Arias

Candamil-Cortés

Jaimes

et al. 2022

Journal of Integrative Bioinformatics

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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 variability, species evolution, and genome size, among others. Because of the way they replicate, LTR retrotransposons are the most common transposable elements in plants, accounting in some cases for up to 80% of all DNA information. To annotate these elements, a reference library is usually created, a curation process is performed, eliminating TE fragments and false positives and then annotated in the genome using the homology method. However, the curation process can take weeks, requires extensive manual work and the execution of multiple time-consuming bioinformatics software. Here, we propose a machine learning-based approach to perform this process automatically on plant genomes, obtaining up to 91.18% F1-score. This approach was tested with four plant species, obtaining up to 93.6% F1-score (Oryza granulata) in only 22.61 s, where bioinformatics methods took approximately 6 h. This acceleration demonstrates that the ML-based approach is efficient and could be used in massive sequencing projects.

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“…Phylogenetic trees were reconstructed using the retrotranscriptase domain of LTR transposons as was previously described (Raharimalala et al 2021). First, each genome was compared against a RT database using CENSOR (Kohany et al, 2006) retaining RT domains with a minimum length of 150 amino-acids.…”

Section: Phylogenetic Reconstruction Of Ltr Transposons Lineagesmentioning

confidence: 99%

Selection signatures and population dynamics of transposable elements in Lima bean

Lozano‐Arce

García

González-García

et al. 2023

Preprint

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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 adaptation followed by Mesoamerican and Andean landraces are largely unknown. The genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Most of the previous genetic analyses in Lima bean have relied on Single Nucleotide Polymorphism (SNP) loci and have ignored transposable elements (TEs) which are a major source of variation in plant genomes. The current availability of high-throughput sequencing technologies enables the collection of whole-genome resequencing (WGS) data to approach intraspecies population dynamics of TEs. The present research collected WGS data from 60 wild and domesticated Lima bean accessions to generate the most complete characterization developed to date of transposable elements and SNP loci in the Lima bean genome. We generated an updated annotation of 223,780 transposable elements in the Lima bean genome. Furthermore, we identified genes and variable TEs affected by selective sweeps. Combining three different approaches, selective sweeps were predicted to generate a set of domestication candidate genes. A small percentage of genes under selection (1.6%) were shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. Up to 25% of the genes with previously reported selective sweeps in common bean were also detected in Lima bean. We also built a catalog of 39,459 TEs with presence-absence variation (PAV). The fact that 75% of these TEs were located close to genes shows their potential to affect gene functions in Lima bean. The genetic structure inferred from variable TEs was consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated Lima bean and its adaptive processes, in particular selection processes during domestication.

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The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Cited by 30 publications

References 66 publications

Ethnopharmacological study of the genus Coffea and compounds of biological importance

Ethnopharmacological study of the genus Coffea and compounds of biological importance

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning

Selection signatures and population dynamics of transposable elements in Lima bean

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