Chloroplast Evolution, Selection and Phylogenomics in Crop and Wild Tropical Plant Species

Submission Deadline: 31 October 2025 View: 29 Submit to Special Issue

Guest Editors

Dr. Filipe de Sousa

Email: filipedeportugal@gmail.com

Affiliation: CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal

Homepage:

Research Interests: Botany, Systematics, Evolution, Phylogenomics

Summary

The genomics era has allowed for the sequencing of vast amounts of molecular data from nuclear and organellar genomes, which in turn enabled the unraveling of long-standing questions in plant science. Whole genome sequencing, as well as target sequencing, normally generates high numbers of sequence reads from chloroplast genomes, which can often be completely assembled into complete circular genomes and fully annotated using open-source online tools.  

Chloroplast genomes are haploid and typically have uniparental inheritance and a highly conserved structure. Chloroplast sequence data has thus been fundamental for molecular barcoding of plants and understanding evolutionary relationships, but the growing availability of whole chloroplast genome sequences has significantly increased phylogenetic resolution. Chloroplast genomes also provide important insights into domestication and hold relevant information for crop improvement.

Advancing the study of chloroplast genomes is essential for understanding evolutionary and diversification patterns in wild and domesticated species. The tropics contain the vast majority of plant species and numerous plants of agricultural interest, including underutilized crops with great potential for food security in a changing environment. For this special issue, we promote original research focusing on tropical and subtropical plant species, or on broader groups containing a significant number of these species. We welcome original research articles, reviews, opinions, and methods articles, based on whole chloroplast or combined nuclear and chloroplast genome data, that show discoveries in plant diversification, evolution, and domestication.

Potential subjects for this topic include:

- speciation and hybridization

- population genetics

- domestication

- signatures of selection and codon usage bias

- trait improvement in crops

- evolution of tropical plants

- plant adaptation to arid environments

Keywords