Practical considerations for plant phylogenomics.

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• The past decade has seen significant advancements in genome sequencing technologies, enabling large-scale data generation across diverse lineages.
• High-throughput sequencing and long-read technologies have propelled the field of phylogenomics, utilizing hundreds to thousands of genes and organellar genomes for evolutionary studies.

Purpose of the Study:

• To review recent advances in plant phylogenomic methods and provide recommendations for project-dependent best practices.
• To guide researchers, particularly newcomers, in selecting appropriate phylogenomic approaches based on specific research questions and available resources.

Main Methods:

• Review of current high-throughput sequencing and long-read technologies applicable to plant phylogenomics.
• Analysis of the costs and benefits associated with different phylogenomic approaches.
• Identification of optimal methodologies for specific plant system challenges, including polyploidy, reticulate evolution, and herbarium material usage.

Main Results:

• Detailed overview of recent progress in plant phylogenomic methodologies.
• Recommendations for best practices tailored to diverse research questions and project scopes.
• Highlighting of unique challenges and opportunities within plant phylogenomics.

Conclusions:

• The selection of phylogenomic methods should be project-dependent, balancing information gained with costs and research questions.
• Addressing challenges like polyploidy and data reusability is crucial for advancing plant phylogenomics.
• Emerging technologies hold promise for future breakthroughs in the field.