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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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 610064, Sichuan, China.

Annals of Botany
|April 27, 2026
PubMed
Summary

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.

Keywords:
RhodiolaAlphaFold 3BiosynthesisEvo2Genome SkimmingSalidroside

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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.