Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide

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.

Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)

“…Our results indicated that, for those species (P. stipuleanatus, P. ginseng, P. quinquefolius and P. notoginseng) whose monophyly has been recognized by previous studies (Zuo et al, 2011(Zuo et al, , 2017 (Coissac et al, 2016;Kan & Cronk, 2008;Kane et al, 2012;Li et al, 2015;Nock et al, 2011;Tontifilippini et al, 2017), although the efficiency of this approach still lacks comprehensive evaluation. Furthermore, (Kane et al, 2012) and Taxus (Fu et al, 2019). However, they failed to fully identify species in Panax (the current study) and New Caledonian Araucaria (Ruhsam et al, 2015), even though there are some gains in discriminatory power.…”

“…Furthermore, the discriminatory power revealed by previous studies sampling multiple intraspecific individuals from multiple congeneric species is largely incongruent. For instance, either complete plastomes or nrDNA sequences were shown to successfully distinguish closely related species in Theobroma (Kane et al, ) and Taxus (Fu et al, ). However, they failed to fully identify species in Panax (the current study) and New Caledonian Araucaria (Ruhsam et al, ), even though there are some gains in discriminatory power.…”

“…The discriminatory power of complete plastomes and nrDNA sequences in plants has been evaluated in some recent studies (e.g., Fu et al, ; Kane et al, ; Ruhsam et al, ; Turner, Paun, Munzinger, Chase, & Samuel, ; Yang et al, ). However, to our knowledge, very few studies have been undertaken which sample multiple individuals from multiple congeneric species.…”

“…The discriminatory power of complete plastomes and nrDNA sequences in plants has been evaluated in some recent studies (e.g., Fu et al, 2019;Kane et al, 2012;Ruhsam et al, 2015;Turner, Paun, Munzinger, Chase, & Samuel, 2016;Yang et al, 2013).…”

Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species

“…For plastomic studies, genetic analyses using plastome fragments have been conducted to reconstruct the phylogeny of the Taxaceae family (e.g., Ran et al, 2010), to develop barcodes to differentiate different species (Gao et al, 2017;Liu et al, 2018), and to explore the demographic history of certain species or species complexes (Ge et al, 2015;Su et al, 2018). Recently, several groups released a number of Taxaceae plastomes Tao et al, 2016;Jia and Liu, 2017), and both intraspecific and interspecific isomeric arrangements have been reported (Hsu et al, 2014;Fu et al, 2019). However, the relative location and genomic organization of the inverted f r a g m e n t s i n T a x a c e a e p l a s t o m e s h a v e n o t b e e n comprehensively studied yet.…”