Phylogenetic Analysis of Cucurbitaceae Genomes

Phylogenetic analysis of Cucurbitaceae genomes integrates plastid and nuclear data to resolve evolutionary relationships within this diverse family of vines and herbaceous plants. Advances in long-read sequencing, Hi-C scaffolding and genome skimming have enabled high-quality assemblies that reveal structural variation, gene family expansions and selective pressures across lineages. By combining whole-chloroplast sequences, single-copy nuclear loci and robust analytical frameworks such as phylogenetic informativeness profiling, researchers have achieved finer resolution of rapid divergences among tribes and clarified genus-level circumscription. These efforts underpin insights into the evolution of key traits—flowering time, fruit morphology and environmental adaptation—and support breeding, conservation and taxonomy of economically important species worldwide.

Research from Nature Portfolio

Recent studies have assembled and compared complete chloroplast genomes across seven wild and cultivated watermelon species, revealing conserved gene order but highly variable non-coding regions. Identification of hypervariable loci such as rps16-trnQ, coupled with numerous simple sequence repeats, has yielded a suite of reliable molecular markers for species delimitation, population genetics and taxonomic barcoding. Phylogenetic trees based on these plastomes have clarified divergence patterns among Citrullus species and highlighted selection on genes involved in photosynthesis and transcriptional regulation.

Genome skimming approaches retrieving plastomes alongside dozens of single-copy nuclear genes have addressed persistent conflicts in tribe-level relationships. By evaluating loci for phylogenetic informativeness and minimising homoplasy risk, researchers have generated highly supported trees that trace rapid early radiations within the family. These analyses have resolved parallel origins of fringed petals and demonstrated the complementary value of plastid versus nuclear data in disentangling complex evolutionary histories.

Phylogenetic Analysis of Cucurbitaceae Genomes publication trend

The graph below shows the total number of articles in phylogenetic analysis of cucurbitaceae genomes across all publications each year (not limited to Nature Index journals).

Technical terms

Chloroplast genome: The circular DNA molecule within chloroplasts encoding genes for photosynthesis and gene expression.

Plastome: Alternative term for the chloroplast genome.

Single-copy region: A section of the plastome present in one copy, classified as large (LSC) or small (SSC).

Inverted repeat (IR): A duplicated segment in the plastome that occurs in opposite orientation, flanking the single-copy regions.

Single-nucleotide polymorphism (SNP): A variation at a single nucleotide position among genomes.

Insertion–deletion (INDEL): A small-scale genomic variation involving the insertion or deletion of bases.

Phylogenomic: Analysis of evolutionary relationships using genome-scale data sets.

Phylogenetic informativeness: A measure of a locus’s ability to resolve divergences at particular evolutionary timescales.

References

1. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. Plants (2024).
2. Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure. Scientific Reports (2023).
3. Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships. Molecules (2018).
4. Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae. Scientific Reports (2020).