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.

Influence of environmental factors on the bathymetric distribution of the flecked box crab Hepatus pudibundus (Herbst, 1785) (Crustacea: Aethroidea) in the Southeastern Brazilian coast

“…The northern coast of São Paulo, in the southeast of Brazil, and specially the Ubatuba region, encompasses a variety of environments such as pristine islands, bays, inlets, sandy and rocky beaches, mangroves, estuaries, and coastal rivers. Due to this spatial heterogeneity, it has a high biodiversity of decapod crustaceans (Mantelatto et al 2018). The sediment in this region is composed by fine or very fine sand and silt and clay, given the low water movement within the area and among the regions (Mahiques et al 1998).…”

Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy

“…Short, easily amplifiable fragments that vary amongst closely related species are sequenced from specimens identified by experts and then used as a reference set to compare with sequences from unidentified or unidentifiable samples (Hebert and Gregory 2005, Hajibabaei et al 2007, Bucklin et al 2011, Bucklin et al 2016, Geiger et al 2016. For animals, the most widely used barcode is cytochrome c oxidase subunit I (COI; Hebert et al 2003), followed by the 16S large subunit ribosomal RNA (16S), another mitochondrial marker (see Mantelatto et al 2017, Collin et al 2018, Collin et al 2019, Morín et al 2019. This approach is useful in a variety of contexts, including identifying components of gut contents and bulk environmental samples.…”

PIDS: A User-Friendly Plant DNA Fingerprint Database Management System

“…The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in determining kinship among individuals and in forensics to identify criminals [3][4][5][6]. In other applications, DNA fingerprints can provide accurate identification at the varieties level [7][8][9], and play important roles in plant breeding [10][11][12]. DNA fingerprints are also commonly used in research on animal evolutionary trends and animal varieties identification [8,13].…”

“…In other applications, DNA fingerprints can provide accurate identification at the varieties level [7][8][9], and play important roles in plant breeding [10][11][12]. DNA fingerprints are also commonly used in research on animal evolutionary trends and animal varieties identification [8,13].…”