Biology subjects

Chenel, E.

Publications and source records attributed to Chenel, E..

2 recordsLinked to original sources

bioRxiv2025

FUSE-PhyloTree: Linking functions and sequence conservation modules of a protein family through phylogenomic analysis

FUSE-PhyloTree is a phylogenomic analysis software for identifying local sequence conservation associated with the different functions of a multi-functional (e.g., paralogous or multi-domain) protein family. FUSE-PhyloTree introduces an original approach that combines advanced sequence analysis with phylogenetic methods. First, local sequence conservation modules within the family are identified using partial local multiple sequence alignment. Next, the evolution of the detected modules and known protein functions is inferred within the familys phylogenetic tree using three-level phylogenetic reconciliation and ancestral state reconstruction. As a result, FUSE-PhyloTree provides a gene tree annotated with both predicted sequence modules and ancestral gene functions, enabling the association of functions with specific sequence regions based on their co-emergence. Availability and ImplementationFUSE-PhyloTree is provided as Docker and Singularity images including all the required software tools. Images, source code, test data, and documentation are available at https://github.com/OcMalde/fuse-phylotree. Supplementary InformationAn illustration of the application of FUSE-PhyloTree to the fibulin protein family is presented in the Appendix.

bioinformatics↗

bioRxiv2024

An unexplored diversity for adaptation of germination to high temperatures in Brassica species

Elevated temperatures inhibit the germination of a concerning number of crop species. One strategy to mitigate the impact of warming temperatures is to identify and introgress adaptive genes into elite germplasm. Diversity must be sought in wild populations, coupled with an understanding of the complex pattern of adaptation across a broad range of landscapes. By investigating the landraces, wild, and feral populations of Algeria, Italy, France, Slovenia, Spain, and Tunisia, we assessed the response of germination to temperature increase in an unexplored diversity of 117 accessions of B. rapa and 66 of B. oleracea. Our results show that both species exhibit heat tolerance to the temperature range tested, especially B. rapa with an increase in speed and uniformity of germination time, as well as an increase in germination rate as temperature increased. As for B. oleracea accessions, the ability to germinate under heat conditions depended on the geographical origin; in particular, southern populations showed a higher germination rate than northern populations, possibly in relation to their warmer climates of origin. These findings highlight the complex interplay between domestication, feralization, and current agronomic practices in shaping germination characteristics in Brassica species.

evolutionary biology↗