Targeted Sequencing in Plant Phylogenomics

Targeted sequencing has emerged as a pivotal methodology in plant phylogenomics, combining cost-effective library preparation with high-throughput sequencing to focus on predefined genomic regions across multiple taxa. By enriching hundreds to thousands of nuclear loci via hybridisation capture, researchers can reconstruct robust phylogenetic trees that resolve both deep nodes and recent radiations. Universal probe sets, such as Angiosperms353, and lineage-specific designs, exemplified by conifer-targeted collections, have standardised data collection, facilitated meta-analyses and promoted cross-study comparability. The approach mitigates challenges posed by large and complex plant genomes, whole-genome duplications and degraded herbarium DNA, enabling the incorporation of historical specimens and under-represented lineages. Targeted sequencing thus supports global efforts in biodiversity assessment, crop domestication studies and conservation genetics. Its flexibility allows simultaneous capture of coding regions and flanking non-coding sequences, yielding information on sequence variation, gene tree discordance and reticulation events. As sequencing costs decline and bioinformatic toolsets mature, targeted phylogenomic data are rapidly transforming our understanding of plant evolutionary history at multiple taxonomic scales.

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Targeted Sequencing in Plant Phylogenomics publication trend

The graph below shows the total number of articles in targeted sequencing in plant phylogenomics across all publications each year (not limited to Nature Index journals).

Technical terms

Targeted sequencing: A method that enriches and sequences selected genomic regions, enabling focused phylogenomic data collection.

Probe set (baits): A collection of oligonucleotide sequences designed to hybridise with target loci during enrichment.

Hyb-Seq (hybridisation sequencing): A workflow combining target enrichment with high-throughput sequencing to capture specific genes.

Single-copy nuclear locus: A gene present in one copy per haploid genome, commonly used to avoid paralogy issues in phylogenetic inference.

Angiosperms353: A universal probe set targeting 353 conserved nuclear genes across flowering plants.

Orthologous loci: Genes in different species that evolved from a common ancestral gene and retain the same function, critical for accurate phylogenetic comparisons.

References

1. Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets. Horticulture Advances (2024).
2. Development of a Target Enrichment Probe Set for Conifer (REMcon). Biology (2024).
3. A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering. Systematic Biology (2018).