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Comparative Lesions Analysis Through a Targeted Sequencing Approach
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Tackling Rapid Radiations With Targeted Sequencing.

Isabel Larridon1,2, Tamara Villaverde3,4,5, Alexandre R Zuntini1

  • 1Royal Botanic Gardens, Kew, Surrey, United Kingdom.

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|January 31, 2020
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Summary
This summary is machine-generated.

Targeted sequencing effectively resolved evolutionary relationships within the difficult C4 Cyperus clade. Both universal and custom kits proved useful, merging data enhanced phylogenetic insights.

Keywords:
C4 Cyperus cladeCyperaceaePlant and Fungal Trees of Lifephylogenomicspolytomytargeted sequencing

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Area of Science:

  • Phylogenetics and evolutionary biology
  • Genomics and bioinformatics
  • Plant systematics

Background:

  • Phylogenetic relationships in angiosperms, particularly within rapidly diversifying groups like Cyperaceae, remain challenging due to high diversification rates and limited marker resolution.
  • Previous studies on the C4 Cyperus clade using Sanger sequencing failed to resolve relationships among species, highlighting the need for advanced genomic approaches.
  • Targeted sequencing offers a powerful solution for resolving species trees in the face of rapid radiations, lineage sorting, and introgression.

Purpose of the Study:

  • To evaluate the efficacy of two targeted sequencing kits (universal Angiosperms-353 and Cyperaceae-specific) in resolving phylogenetic relationships within the C4 Cyperus clade.
  • To compare the data recovery, overlap, and efficiency of general versus custom targeted sequencing approaches.
  • To investigate the evolutionary history of morphology and taxonomic realignments within the C4 Cyperus clade.

Main Methods:

  • Sequencing of targeted loci using both the universal Angiosperms-353 and a Cyperaceae-specific kit.
  • Analysis of sequence data to assess data overlap and kit efficiency.
  • Phylogenetic inference using a summary species tree method and a concatenated maximum likelihood approach to test shallow-level relationship resolution.

Main Results:

  • Both targeted sequencing kits yielded high resolution and support for phylogenetic relationships within the C4 Cyperus clade.
  • High levels of missing data disproportionately impacted the concatenated maximum likelihood approach compared to the summary species tree method.
  • Targeted sequencing revealed the polyphyletic nature of the segregate genus Alinula and identified the Cyperus margaritaceus-Cyperus niveus complex as sister to the core C4 Cyperus clade.

Conclusions:

  • Targeted sequencing is a powerful tool for resolving rapid radiations and complex phylogenetic histories, as demonstrated in the C4 Cyperus clade.
  • Data from universal and family-specific targeted sequencing kits can be merged, and universal kits can be as effective as custom kits.
  • The study provides new insights into the evolution of morphology and taxonomy within the C4 Cyperus clade, necessitating taxonomic revisions.