DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline

Abstract

DNA barcoding has emerged as an efficient tool for taxonomy and other biodiversity fields. The vast and speciose group of decapod crustaceans is not an exception in the current scenario and comparing short DNA fragments has enabled researchers to overcome some taxonomic impediments to help broadening knowledge on the diversity of this group of crustaceans. Brazil is considered as an important area in terms of global marine biodiversity and some regions stand out in terms of decapod fauna, such as the São Paulo coastline. Thus, the aim of this study is to obtain sequences of the mitochondrial markers (COI and 16S) for decapod crustaceans distributed at the São Paulo coastline and to test the accuracy of these markers for species identification from this region by comparing our sequences to those already present in the GenBank database. We sampled along almost the 300 km of the São Paulo coastline from estuaries to offshore islands during the development of a multidisciplinary research project that took place for 5 years. All the species were processed to obtain the DNA sequences. The diversity of the decapod fauna on the São Paulo coastline comprises at least 404 species. We were able to collect 256 of those species and sequence of at least one of the target genes from 221. By testing the accuracy of these two DNA markers as a tool for identification, we were able to check our own identifications, including new records in GenBank, spot potential mistakes in GenBank, and detect potential new species.

Keywords:

• Barcode
• biodiversity
• Brazil
• COI mtDNA
• 16S rDNA

Acknowledgements

Our special thanks to Fernando J. Zara, Rogério C. Costa and Antonio L. Castilho as other co-researchers of the BIOTA-FAPESP and CAPES-CIMar projects, and their respective team of students, who helped with sampling and making fresh material available for molecular procedures. We express our sincere thanks to all members of the LBSC and to all colleagues who generated some of the sequences throughout this project (Abner Carvalho-Batista, Ana Luiza Vera-Silva, Bárbara Prado, Caio Oliveira, Carla Kuhl, Douglas Peiró, Edvanda Souza-Carvalho, Emiliano Ocampo, Fabrício Carvalho, Gabriela Zanarotti, Isabela Leone, Juliana Paixão, Keity Nishikawa, Mateus Lopes, Sabrina Morilhas Simões, Sarah Teodoro and Silvia Mandai). Finally, we would particularly like to thank Dr. Leonardo Pileggi, who collaborated in the construction and implementation phases of the BIOTA-FAPESP project.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.

Additional information

Funding

This work was supported by São Paulo Research Foundation [Proc. 2010/50188-8] in the program BIOTA-FAPESP. Additional and supplementary support came from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – CAPES (Ciências do Mar II Proc. 2005/2014 - 23038.004308/201414) and the Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq (Research Scholarship PQ 304968/2014-5), all under FLM coordination.