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. 2018;41(3):661-670.
doi: 10.1590/1678-4685-GMB-2017-0282.

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

Renato A Ferreira de Lima  1 , Alexandre Adalardo de Oliveira  1 , Gabriel Dalla Colletta  2   3 , Thiago Bevilacqua Flores  2   3 , Rubens L Gayoso Coelho  4 , Pedro Dias  4 , Gabriel Ponzoni Frey  1 , Amaia Iribar  5 , Ricardo Ribeiro Rodrigues  2 , Vinícius Castro Souza  2 , Jérôme Chave  5
Affiliations

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

Renato A Ferreira de Lima et al. Genet Mol Biol. 2018.

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.

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Figures

Figure 1
Figure 1. Venn diagrams of the number of species with sequences for the combination of (a) rbcL + matK + ITS region and (b) rbcL + matK + psbA-trnH.
Figure 2
Figure 2. The sampling priority level in future sequencing for each family of the SP tree flora, plotted against its phylogenetic hypothesis. The priority level was defined based on the representativeness of DNA barcodes within the family and the proportion of threatened and endemic species without barcodes.
Figure 3
Figure 3. Increase of the number of (a) species, (b) genera and (c) families across time with respect to the ten DNA markers considered in this study. Bold lines are the best fit of the logistic function to the accumulated number of sequences or taxa. Dashed lines are the total of taxa in the SP tree flora. Dates are aggregated in trimesters and the fit of functions to the accumulated number of taxa was carried out only from mid 1995 on.
See this image and copyright information in PMC

References

    1. Adams KL, Palmer JD. Evolution of mitochondrial gene content: Gene loss and transfer to the nucleus. Mol Phylogenet Evol. 2003;29:380–395. - PubMed
    1. Alvares CA, Stape JL, Sentelhas PC, Moraes G, Leonardo J, Sparovek G. Köppen’s climate classification map for Brazil. Meteor Z. 2013;22:711–728.
    1. Armstrong KF, Ball SL. DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc Lond B Biol Sci. 2005;360:1813–1823. - PMC - PubMed
    1. Bolson M, Smidt EC, Brotto ML, Silva-Pereira V. ITS and trnH-psbA as efficient DNA barcodes to identify threatened commercial woody angiosperms from Southern Brazilian Atlantic rainforests. PLoS One. 2015;10:e0143049. - PMC - PubMed
    1. Caiafa AN, Martins FR. Taxonomic identification, sampling methods, and minimum size of the tree sampled: Implications and perspectives for studies in the Brazilian Atlantic Rainforest. Funct Ecosyst Comm. 2007;1:95–104.

Internet Resources

    1. Oliveira-Filho AT. NeoTropTree, Flora arbórea da Região Neotropical: Um banco de dados envolvendo biogeografia, diversidade e conservação. Universidade Federal de Minas Gerais; 2014. http://www.neotroptree.info/
    1. Thiers B. Index herbariorum: A global directory of public herbaria and associated staff. The New York Botanical Garden; 2015. http://sweetgum.nybg.org/science/ih/