Assessing candidate DNA barcodes for Chinese and internationally traded timber species

Abstract

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH–psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH–psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family‐level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH–psbA+ITS2 are required to provide broader discrimination power. These newly‐generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

“…Furthermore, the China Plant BOL Group recommended that the nuclear internal transcribed spacer (nrITS) be incorporated into the core plant barcode (Li et al, 2011). There are numerous successful cases of using traditional standard DNA barcodes (including the multilocus combination of plastid rbc L + mat K + trn H‐ and nrITS) or other specific barcodes (Bruni et al, 2010; Hu et al, 2022; Liu et al, 2011, 2018; Xu et al, 2018). However, other research has shown that traditional standard DNA barcodes have tremendous limitations in species discrimination, primarily attributed to a lack of variation in many taxa, especially in evolutionarily young and rapidly radiated taxa (Spooner, 2009; van Velzen et al, 2012; Yan et al, 2015).…”

DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes

“…Currently, the mitochondrial gene cytochrome oxidase I ( COI ) has been proven to be an ideal DNA barcode for animals (Burns et al, 2008; Kerr et al, 2007; Kim et al, 2012), whereas this DNA region is not suitable for plant identification due to the low substitution rates of plant mitochondrial DNA (Cho et al, 2004; Duminil, 2014; Kress et al, 2005). Alternatively, plastid sequences ( rbcL and matK ) and the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) have been recommended as core barcodes for plants, and plastid sequences ( trnH‐psbA and trnL ‐F) have been recommended as supplementary barcodes (CBOL Plant Working Group, 2009; Chase et al, 2007; Hollingsworth et al, 2011; Hu et al, 2022; Kress et al, 2009; Lahaye et al, 2008; Li et al, 2009; Li, Gao, et al, 2011; Li, Liu, et al, 2011; Tonti‐Filippini et al, 2017; Vijayan et al, 2009; Worthy et al, 2022). The application of DNA barcoding has been successfully used in the problem of species identification in a large number of taxa (e.g., Giudicelli et al, 2015; Gogoi & Bhau, 2018; Liu et al, 2011, 2018).…”

Plant DNA barcode library for native flowering plants in the arid region of northwestern China

“…The arid region covers nearly 25% of the territory in China. However, the DNA barcode reference libraries in China are concentrated primarily in southern biodiversity‐rich areas, for example subtropical forests (Liu et al, 2015), mangrove forests (Mao et al, 2021) and timber species (Hu et al, 2022), with limited DNA barcode data for northwestern arid regions.…”

“…(i) Barcoding gap method: intra‐ and interspecific genetic distances were calculated for each barcode ( rbcL , matK , ITS and ITS2) separately by using “DistanceMatrix” in the R (R Core Team, 2019) package decipher (Wright, 2016). Barcode gaps existed for species with lower maximum intraspecific distances than with minimum interspecific distances (Gill et al, 2019; Hu et al, 2022). (ii) All‐to‐all blast search method (Kelly et al, 2011): based on blast version 2.10.1+ all barcode sequences served as both reference and query databases.…”