Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
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-...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12862-023-02185-z |
| _version_ | 1827581843541590016 |
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| author | Mustafa Raza Edgardo M. Ortiz Lea Schwung Gentaro Shigita Hanno Schaefer |
| author_facet | Mustafa Raza Edgardo M. Ortiz Lea Schwung Gentaro Shigita Hanno Schaefer |
| author_sort | Mustafa Raza |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-03-08T22:42:09Z |
| format | Article |
| id | doaj.art-3a01de4ee0954c7fb6736f04d2c3a227 |
| institution | Directory Open Access Journal |
| issn | 2730-7182 |
| language | English |
| last_indexed | 2024-03-08T22:42:09Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj.art-3a01de4ee0954c7fb6736f04d2c3a2272023-12-17T12:04:32ZengBMCBMC Ecology and Evolution2730-71822023-12-0123111310.1186/s12862-023-02185-zResolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelinesMustafa Raza0Edgardo M. Ortiz1Lea Schwung2Gentaro Shigita3Hanno Schaefer4Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM)Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM)Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM)Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM)Plant Biodiversity Research, Dept. Life Science Systems, Technical University of Munich (TUM)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).https://doi.org/10.1186/s12862-023-02185-zCaptusCoalescentConcatenationCucurbitaceaeHybPiperSECAPR |
| spellingShingle | Mustafa Raza Edgardo M. Ortiz Lea Schwung Gentaro Shigita Hanno Schaefer Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines BMC Ecology and Evolution Captus Coalescent Concatenation Cucurbitaceae HybPiper SECAPR |
| title | Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines |
| title_full | Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines |
| title_fullStr | Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines |
| title_full_unstemmed | Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines |
| title_short | Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines |
| title_sort | resolving the phylogeny of thladiantha cucurbitaceae with three different target capture pipelines |
| topic | Captus Coalescent Concatenation Cucurbitaceae HybPiper SECAPR |
| url | https://doi.org/10.1186/s12862-023-02185-z |
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