ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests

Abstract

The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the ‘best close match’ test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.

Plant DNA barcodes: Applications today and in the future

“…Nithaniyal et al () used the standard plant DNA barcode markers to accurately identify wood samples collected at timber processing plants in Andhra Pradesh and Tamil Nadu. This same success was demonstrated in timber species found in Araucaria rain forests of the southern Atlantic coast of Brazil (Bolson et al, ), which contains many threatened species of trees with high commercial importance, especially in the family Lauraceae. Most recently, DNA barcoding was employed to monitor illegal timber trade in the biodiversity hotspot of Madagascar, where species of Dalbergia (Fabaceae), the rosewoods, are under threat.…”

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

“…Numerous studies have suggested that four standard barcodes, mat K, rbc L, trn H- psb A, and ITS , should be used as core barcode markers for the molecular identification of land plants (Hollingsworth et al, 2011; Li et al, 2011). In addition to choosing DNA barcoding fragments, collecting many individuals from different populations within a species is also important for establishing a reference database for universal application (Bolson et al, 2015; Guo et al, 2016). …”

High‐resolution biomonitoring of plant pathogens and plant species using metabarcoding of pollen pellet contents collected from a honey bee hive

“…After running the metaResultExtractor.pl script to scan for gen- again, they should be interpreted cautiously until identification of such organisms can be confirmed with a combinatory standardized method (e.g., qPCR) or additional genetic markers due to the limited resolution power of the ITS1 for certain groups (Inderbitzin et al, 2011;Inderbitzin & Subbarao, 2014;Martin et al, 2012;Peever et al, 2004;Taheri, Chatterton, Foroud, Gossen, & McLaren, 2017;Zitnick-Anderson et al, 2018). For instance, the elongation factor 1α is better suited for identification of F. sporotrichioides (Taheri et al, 2017;Zitnick-Anderson et al, 2018), and the trnH-psbA spacer is gaining in popularity for assisting plant identification (Bolson, Smidt, Brotto, & Silva-Pereira, 2015;Kress & Erickson, 2007).…”