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Repurposing genome skimming data for non-model plant functional phylogenetics: a case study in Rhodiola
Hao He1,2, Fu-Sheng Yang3,4,5, Yu-Xiang Zhang1,2
1Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Southwest Bio-resources R&D Key Laboratory of Sichuan Province, Chengdu Botanical Garden-Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.
Genome skimming successfully revealed functional gene evolution in Rhodiola, identifying genes under purifying selection and those adapting to environmental changes. This method aids non-model plant research.
Area of Science:
- Genomics and Evolutionary Biology
- Plant Molecular Evolution
Background:
- Investigating functional gene evolution in non-model plants is challenging due to limited genomic resources.
- Extreme environments pose unique evolutionary pressures on plant taxa.
- The salidroside biosynthesis pathway in Rhodiola serves as a model for studying adaptation.
Purpose of the Study:
- To assess the utility of genome skimming for studying functional gene evolution in non-model plants.
- To test predictions regarding selection pressures on salidroside biosynthesis genes in Rhodiola.
- To explore the relationship between gene evolution, environmental factors, and protein binding properties.
Main Methods:
- Genome skimming integrated with codon-based selection analyses and environmental variable analysis.
- Utilized deep learning tools (Evo2, AlphaFold 3) for conservation scoring and protein structure prediction.
- Phylogenetic signal analyses (RASP) examined gene evolution associations with climatic/edaphic factors across 18 Rhodiola species.
Main Results:
- Successfully retrieved 37 target genes with high recovery rates.
- Identified six genes (e.g., 4HPAAS, 4HPAR2) under strong purifying selection, showing high structural conservation and correlating with temperature and precipitation gradients.
- Divergence time estimates suggest functional gene diversification during the Pliocene-Quaternary, linked to Qinghai-Tibet Plateau uplift.
- Highlighted three candidate genes (4HPAR2, UGT10, UGT26) with lineage-specific selective constraint shifts tied to environmental gradients.
Conclusions:
- Genome skimming, coupled with computational analyses, is effective for testing evolutionary hypotheses in non-model plants.
- Identified candidate genes for functional and ecological validation in Rhodiola evolution.
- Provides a framework for similar studies in other under-resourced plant lineages.
