Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil

Abstract

DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.

Chloroplast Genome Sequences and Comparative Analyses of Combretaceae Mangroves with Related Species

“…MatK gene is identified to be essential for plant cell survival, and the expression of it needs to be tightly regulated to prevent detrimental effects and establishes another link between leaf variegation and chloroplast translation [ 57 ]. For the studies of plant systematics, the matK gene is the high selectively used gene as the DNA barcoding fragment for plants [ 58 ].…”

Unravelling the plant diversity of the Amazonian canga through DNA barcoding

“…The implementation of DNA barcoding approaches for plants was slower and more complex than for animal species (see Fazekas et al, 2009). Nevertheless, the importance of DNA barcodes in surveying plant diversity has been extensively acknowledged during the last decade, despite the inherent difficulties of establishing universal and practical methodologies to be applied in a wide range of taxonomic groups from different ecosystems, considering the particularities observed in several taxa (Hollingsworth et al, 2016;Kress, 2017;Lima et al, 2018). Therefore, we initially tested eight of the most used DNA barcode regions (Fazekas et al, 2008;Lima et al, 2018).…”

“…Nevertheless, the importance of DNA barcodes in surveying plant diversity has been extensively acknowledged during the last decade, despite the inherent difficulties of establishing universal and practical methodologies to be applied in a wide range of taxonomic groups from different ecosystems, considering the particularities observed in several taxa (Hollingsworth et al, 2016;Kress, 2017;Lima et al, 2018). Therefore, we initially tested eight of the most used DNA barcode regions (Fazekas et al, 2008;Lima et al, 2018). This evaluation was important to establish rbc L and ITS2 as the best markers covering the principles of standardization, minimalism and scalability (Hollingsworth et al, 2011), considering the vast diversity of vascular plants of the Serra dos Carajás, as recently inventoried by the FCC project (Viana et al, 2016;Mota et al, 2018;Salino et al, 2018).…”

“…It is important to mention that the Melastomataceae was recorded as the fifth most diverse angiosperm family in the FCC, with a total of 41 species (Rocha et al, 2017;Mota et al, 2018). Lima et al (2018) also reported low rates of amplification success for rbc L and mat K when barcoding tree species of Melastomataceae, one of the most species-rich families in the flora of the Brazilian state of São Paulo. Although these authors could overcome such a problem with the plastid markers by using the ITS region, the results we obtained here for the four barcoded species of Melastomataceae with ITS2 were only slightly better than for rbc L (one barcoded species), considering the universal protocols used.…”

Using near-infrared spectroscopy to discriminate closely related species: A case study of neotropical ferns

“…The high predictive power of FT-NIR at discriminating fern species, presented here, is superior to that observed for this lineage using a single region of two combined DNA barcodes, for which the best performance was 75 % correct predictions (Li et al 2011; Wang et al 2016). Identifying ferns and other plant groups using DNA barcoding is also an expensive technique and different lineages require specific combinations of molecular markers, which can make this technique complicated (Li et al 2011; Lima et al 2018). However, barcoding gametophytes has shown promising results for identifying species of ferns, which represents a great contribution to what is known about the evolution of this group (Schneider and Schuettpelz 2006).…”