An updated and extended version of the Melastomataceae probe set for target capture
Abstract Premise A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and oth...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-01-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11564 |
| _version_ | 1827348014283358208 |
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| author | Léo‐Paul M. J. Dagallier Fabián A. Michelangeli |
| author_facet | Léo‐Paul M. J. Dagallier Fabián A. Michelangeli |
| author_sort | Léo‐Paul M. J. Dagallier |
| collection | DOAJ |
| description | Abstract Premise A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae. Methods In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version. Results The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery. Discussion This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available. |
| first_indexed | 2024-03-08T00:03:41Z |
| format | Article |
| id | doaj.art-133332a6ccea42bca8fdd53d318b17a5 |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-03-08T00:03:41Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-133332a6ccea42bca8fdd53d318b17a52024-02-17T10:50:29ZengWileyApplications in Plant Sciences2168-04502024-01-01121n/an/a10.1002/aps3.11564An updated and extended version of the Melastomataceae probe set for target captureLéo‐Paul M. J. Dagallier0Fabián A. Michelangeli1Institute of Systematic Botany New York Botanical Garden Bronx New York USAInstitute of Systematic Botany New York Botanical Garden Bronx New York USAAbstract Premise A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae. Methods In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version. Results The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery. Discussion This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.https://doi.org/10.1002/aps3.11564Hyb‐SeqMelastomataceaephylogenomicsphylogenytarget capturetranscriptome |
| spellingShingle | Léo‐Paul M. J. Dagallier Fabián A. Michelangeli An updated and extended version of the Melastomataceae probe set for target capture Applications in Plant Sciences Hyb‐Seq Melastomataceae phylogenomics phylogeny target capture transcriptome |
| title | An updated and extended version of the Melastomataceae probe set for target capture |
| title_full | An updated and extended version of the Melastomataceae probe set for target capture |
| title_fullStr | An updated and extended version of the Melastomataceae probe set for target capture |
| title_full_unstemmed | An updated and extended version of the Melastomataceae probe set for target capture |
| title_short | An updated and extended version of the Melastomataceae probe set for target capture |
| title_sort | updated and extended version of the melastomataceae probe set for target capture |
| topic | Hyb‐Seq Melastomataceae phylogenomics phylogeny target capture transcriptome |
| url | https://doi.org/10.1002/aps3.11564 |
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