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.
Highlights
DNA barcoding consists in telling apart organisms based on specific regions of their DNA
We combine sequences from a large sequencing effort carried out locally with sequences retrieved from GenBank to answer the following questions: (i) How many barcodes are available for the São Paulo tree flora, has this number increased through time, and which taxa still remain underrepresented? (ii) Which DNA markers are better represented among São Paulo tree species? (iii) What proportion of trees in São Paulo forests already has barcode sequences available? (iv) Do species with larger geographical distribution tend to have more information on DNA barcodes? In the light of our results, we propose directions to future sequencing efforts to achieve a more complete DNA reference library for São Paulo, which could be applied to other tropical areas
The first DNA barcode accession for SP trees was an rbcL sequence submitted to GenBank in December 1993 for Trema micrantha, a widespread Neotropical pioneer
Summary
DNA barcoding consists in telling apart organisms based on specific regions of their DNA. Devised as a tool to identify microorganisms, such as bacteria (Woese et al, 1990), its use can be extended to all life forms, as long as DNA can be extracted from living, dead or fossil material. This approach developed rapidly for animals, for which one gene fragment, the mitochondrial cytochrome oxidase I (COI), was shown to be a reliable barcode in important lineages (Hebert et al, 2003). The chloroplastic rbcL and matK markers were the first proposals of barcodes for land plants (CBOL Plant Working Group, 2009), with further suggestions for the inclusion of ITS region and psbA-trnH as core barcodes (Gonzalez et al, 2009; Hollingsworth, 2011; Li et al, 2011)
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