A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.
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1.65 MB
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Resource type
Journal article
Date published
December 21, 2021
Abstract
Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of and related species, as well as aid molecular identification applications.
Funder
| Funder name | Awards |
Horizon 2020, European Union | MSCA-ITN Plant.ID, Grant Agreement No. 765000. |
Marie Skłodowska-Curie Actions | MSCA Individual Fellowship Yamnomics, Grant Agreement H2020-EU.1.3.2. |
Journal title
Scientific Reports
Volume
11
Article number
24347
Publisher
Springer Science and Business Media LLC
Place of publication
Berlin/Heidelberg, Germany
eISSN
2045-2322
Date accepted
November 18, 2021
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Rights statement
In Copyright