Abstract
Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by “trnQ-IRs”. These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.
Highlights
The plastid genomes of photosynthetic land plants are generally characterized by two unequal single-copy regions separated by a pair of canonical inverted repeats (IRs)[1]
Incorporating the previously elucidated plastomes of other Taxaceous genera, this study aims to address the following questions: 1) Do plastomic characteristics—in terms of genome size, gene content, nucleotide compositions, and structure—vary across the Taxaceae? 2) Are isomeric plastomes common in Taxus? If yes, do their relative abundances vary among species and/or populations? 3) Are whole plastome sequences suitable super-barcodes for discriminating yew species? If not, are there any special plastid genes/intergenic spacers that are promising barcoding loci for identifying yew species?
A pair of short inverted repeats with a trnQ-UUG in each copy is common in Taxaceae, with Taxus and Amentotaxus having the shortest and longest trnQ-IRs, respectively (Table 1)
Summary
The plastid genomes (plastomes) of photosynthetic land plants are generally characterized by two unequal single-copy regions separated by a pair of canonical inverted repeats (IRs)[1]. An approach combining the best use of single-locus barcodes and super-barcodes for efficient plant identification was suggested for selected groups of taxa, including specific barcodes that could distinguish closely related plants at the species and population levels[17]. Taxaceae includes six genera (Amentotaxus, Austrotaxus, Cephalotaxus, Pseudotaxus, Taxus, and Torreya) and about 30 species of evergreen trees or shrubs, distributed mainly in the Northern Hemisphere[31,32]. This cupressophyte family likely diverged from its closest sister, Cupressaceae, during the Early Triassic[32,33].
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