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Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines. | LitMetric

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines.

BMC Ecol Evol

Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM), Emil-Ramann-Str. 2, D-85354, Freising, Germany.

Published: December 2023

AI Article Synopsis

  • - The study evaluates the performance of a new pipeline called Captus against established ones (HybPiper and SECAPR) for analyzing various sequencing data in phylogenomic research, specifically focusing on the genus Thladiantha.
  • - Captus demonstrates better results in terms of computation time, locus recovery per sample, and number of informative sites, while producing species trees with fewer gene conflicts, although topological differences among pipelines remain minimal.
  • - The findings indicate that Captus is the most efficient pipeline for phylogenomic analysis of Thladiantha, as it effectively generates a higher number of aligned gene trees that align with the overall species tree topology.

Article Abstract

Background: Despite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana.

Results: Our pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments, and (4) the topology of the nuclear and plastid phylogenies. Additionally, the simulated reads derived from the genome of Arabidopsis thaliana were used to evaluate the accuracy and completeness of the recovered loci. In terms of computation time, locus recovery per sample, and informative sites, Captus outperforms HybPiper and SECAPR. The resulting topologies of Captus and SECAPR are identical for coalescent trees but differ when trees are inferred from concatenated alignments. The HybPiper phylogeny is similar to Captus in both methods. The nuclear genes recover a deep split of Thladiantha in two clades, but this is not supported by the plastid data.

Conclusions: Captus is the best choice among the three pipelines in terms of computation time and locus recovery. Even though there is no significant topological difference between the Thladiantha species trees produced by the three pipelines, Captus yields a higher number of gene trees in agreement with the topology of the species tree (i.e., fewer genes in conflict with the species tree topology).

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10714463PMC
http://dx.doi.org/10.1186/s12862-023-02185-zDOI Listing

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