DNA Barcoding Of The Genus Fargesia

Fargesia,the largest genus within the temperate bamboos tribe Arundinarieae(Poaceae:Bambusoideae),has more than 90 species,mainly distributed in the mountains of Southwest China.These bamboos have considerable ecological and economic value,they are essential components of the alpine forest ecosystem,which provides food and habitat for many endangered animals,including the giant panda.However,due to the long flowering intervals and variable morphological characteristics,it is peculiarly difficult to identify Fargesia species depending on morphology alone.Moreover,the discriminatory power of standard DNA barcodes(matK,rbcL,trnH-psbA)in identifying bamboos was very low,it is far from adequate for achieving DNA identification in bamboos.With the development of new sequencing approaches,complete plastid genome(plastome)and ribosomal DNA(nrDNA)have been proposed as candidates for the next generation of DNA barcodes(plant DNA barcode 2.0)to increase the power of plant species discrimination,also known as ultrabarcode.However,ultra-barcode has not been tested in bamboos.In this study,we collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastome and nrDNA sequences compared to the standard barcodes.We newly obtained 136 plastomes and 110 nrDNA sequences for Fargesia.Another,7 individuals with whole plastomes sequences and 22 individuals with ITS sequences were downloaded from the GenBank.We constructed seven datasets to compare the discriminatory power.To evaluate species discrimination success,we used two approaches:tree-based methods and distance-based analysis.For DNA barcodes based on plastid data,Three-marker combinations of the plastid barcodes(matK+rbcL+trnH-psbA)showed the lowest discriminatory power in Fargesia with the discrimination rate at 5.7%,the complete plastomes and LSC region showed the highest discrimination rate at 28.6%.Though the complete plastome can substantially increase discriminatory power compared to standard plastid barcodes,the slow substitution rates of Fargesia plastomes result in the discrimination rate remaining low.We also found nuclear markers performed better than plastid markers,and even ITS alone had higher discriminatory power(47.2%)than complete plastome.It showed a moderate improvement when comparing nrDNA to ITS,and nrDNA sequences show a moderate improvement compared to ITS with 57.7%of species distinguished.Our analysis found that the complete plastome and nrDNA sequences had substantially higher discriminatory power than the standard barcodes in Fargesia.However,neither of these sequences could discriminate all the sampled species,possibly due to the long generation time and complex evolutionary history of Fargesia.Therefore,our results reinforce the need to access multiple nuclear markers in species discrimination in plants.