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PremiseUnderstanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up‐front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages. MethodsWe designed an Orchidaceae target capture bait set for 963 single‐copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae. ResultsBetween 1,518,041 and 87,946,590 paired‐end 150‐base reads were generated for target‐enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. DiscussionThe Orchidaceae963 kit will enable greater accessibility and utility of next‐generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.
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Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq
PremiseApocynaceae is the 10th largest flowering plant family and a focus for study of plant–insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non‐model taxa, such as Apocynaceae. MethodsTranscriptomes were used to design probes for targeted sequencing of putatively single‐copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. ResultsFrom 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent‐based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genusApocynum. Intraspecific comparison ofElytropus chilensisindividuals revealed numerous single‐nucleotide polymorphisms with potential for use in population‐level studies. DiscussionCommunity use of this Hyb‐Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
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- PAR ID:
- 10455727
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Applications in Plant Sciences
- Volume:
- 8
- Issue:
- 11
- ISSN:
- 2168-0450
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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