Calceolariaceae809: A bait set for targeted sequencing of nuclear loci
Abstract Premise The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-11-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11557 |
| _version_ | 1797391439065251840 |
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| author | Nicolas Medina David C. Tank Anahí Espíndola |
| author_facet | Nicolas Medina David C. Tank Anahí Espíndola |
| author_sort | Nicolas Medina |
| collection | DOAJ |
| description | Abstract Premise The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives. Methods We developed a bioinformatic workflow to use incomplete, low‐coverage genomes of 10 Calceolaria species to identify single‐copy loci suitable for phylogenetic studies and design baits for targeted sequencing. Results Our approach resulted in the identification of 809 single‐copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates. Discussion Our results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus. |
| first_indexed | 2024-03-08T23:32:38Z |
| format | Article |
| id | doaj.art-504148ac93b14495890b752d41398dcd |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-03-08T23:32:38Z |
| publishDate | 2023-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-504148ac93b14495890b752d41398dcd2023-12-14T11:06:16ZengWileyApplications in Plant Sciences2168-04502023-11-01116n/an/a10.1002/aps3.11557Calceolariaceae809: A bait set for targeted sequencing of nuclear lociNicolas Medina0David C. Tank1Anahí Espíndola2Department of Entomology University of Maryland College Park Maryland 20742‐4454 USADepartment of Botany and Rocky Mountain Herbarium University of Wyoming Laramie Wyoming 82071 USADepartment of Entomology University of Maryland College Park Maryland 20742‐4454 USAAbstract Premise The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives. Methods We developed a bioinformatic workflow to use incomplete, low‐coverage genomes of 10 Calceolaria species to identify single‐copy loci suitable for phylogenetic studies and design baits for targeted sequencing. Results Our approach resulted in the identification of 809 single‐copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates. Discussion Our results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus.https://doi.org/10.1002/aps3.11557Andesbioinformatic pipelineCalceolariaLamialesphylogenomicstarget capture |
| spellingShingle | Nicolas Medina David C. Tank Anahí Espíndola Calceolariaceae809: A bait set for targeted sequencing of nuclear loci Applications in Plant Sciences Andes bioinformatic pipeline Calceolaria Lamiales phylogenomics target capture |
| title | Calceolariaceae809: A bait set for targeted sequencing of nuclear loci |
| title_full | Calceolariaceae809: A bait set for targeted sequencing of nuclear loci |
| title_fullStr | Calceolariaceae809: A bait set for targeted sequencing of nuclear loci |
| title_full_unstemmed | Calceolariaceae809: A bait set for targeted sequencing of nuclear loci |
| title_short | Calceolariaceae809: A bait set for targeted sequencing of nuclear loci |
| title_sort | calceolariaceae809 a bait set for targeted sequencing of nuclear loci |
| topic | Andes bioinformatic pipeline Calceolaria Lamiales phylogenomics target capture |
| url | https://doi.org/10.1002/aps3.11557 |
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