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.
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