DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China

Abstract

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH–psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH–psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis–Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.

Development of high‐resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis

“…DNA barcodes show a relatively variable species discrimination efficiency in different plants (Gogoi & Bhau, 2018;Hollingsworth et al, 2011;Liu et al, 2017;Sun et al, 2015Sun et al, , 2012, and more DNA barcodes for specieslevel resolution have been developed and tested (Dong et al, 2015;Song et al, 2017). At present, the devel opment of universal primers for highly variable regions relies on the availability of sequences for different species.…”

Automated identification of Lauraceae by scale-invariant feature transform

“…7a, eleven genera are blanched into 4 groups. Machilus belonged to the same group with Cinnamomum and both the species are in very close distance to each other, although in the actual phylogenetic relationship [5,6], Machilus is close to Phoebe. In practice, with microscopic inspection, some species in Machilus are known to be difficult to be distinguished from those of Phoebe, even by skilled wood anatomists.…”

“…With the classification by SIFT depending only on the crosssectional morphological features of wood, it is not surprising that both at the genus and species levels, the relative numerical distances of each genus and species are slightly different from the reported phylogenetic relationships [5,6]. According to Liu et al [5], who studied the phylogenic relationships of 409 individuals representing 133 species of 12 genera in the Lauraceae using DNA barcoding, 44 individuals from the ten species were misclassified by the form taxonomists.…”

“…According to Liu et al [5], who studied the phylogenic relationships of 409 individuals representing 133 species of 12 genera in the Lauraceae using DNA barcoding, 44 individuals from the ten species were misclassified by the form taxonomists. This supports the fact that the morphological features of the Lauraceae are indeed complex to be Table 2 and Fig.…”

“…More recently, identification methods are gradually expanding to new techniques such as DNA-based identification [2][3][4][5][6] and spectroscopy-based chemometrics [7][8][9][10][11][12]. These methods are used primarily for specific purposes.…”