DNA barcoding of macrofauna act as a tool for assessing marine ecosystem Sivaraj Sigamani a, ⁎, Murugesan Perumal a , Gopi Alagiri Thivakaran b , Balasubramanian Thangavel a , Kathiresan Kandasamy a , Angel Borja c a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India b Gujarat Institute of Desert Ecology, Gujarat, India c AZTI-Tecnalia - Marine Research Division, Spain abstract article info Article history: Received 7 May 2016 Received in revised form 9 July 2016 Accepted 11 July 2016 Available online xxxx Nowadays, marine ecosystem monitoring and assessment are increasingly depending on variety of molecular tools. With these background, DNA barcoding play a key role in species identification with increasing speed and accuracy, and although the suitability for developing genetic tools like genomic AMBI (gAMBI). Presently we have submitted 13 benthic polychaete species using mtCOI to GenBank. Of these, nine species were newly submitted, and hence they act as a benchmark and reference organism for identifying respective polychaete spe- cies worldwide in the near future. Based on that, our study results tend to be helpful for motivating among the researcher in order to implementing the genomic AMBI (gAMBI). © 2016 Elsevier Ltd. All rights reserved. Keywords: DNA barcoding Marine ecosystem Molecular methods Genetic tool Genomic AMBI 1. Introduction In response to urbanization and increasing human impact on our oceans (Claudet and Fraschetti, 2010; Lotze, 2010), legislation has been implemented world-wide to protect, conserve or enhance marine ecosystems. Thus, ecologists have realised the importance of ecological health monitoring/assessment, and this fact has led researchers to in- vestigate new and cost-effective methods to monitor and assess marine ecosystem (Frolov et al., 2013). Usually, physico-chemical parameters and benthic community structure are used for assessing the health of an ecosystem; while former reflect conditions only at the time of sam- pling and latter indicates the present conditions and also during yester- years (Apitz et al., 2006). As an alternative to this, genomics, the science that uses nucleotide sequences (DNA or RNA) to analyse biological sys- tems represents the most likely source of innovation in marine monitor- ing programs. There is a great potential for the development of genomic techniques for in situ detection in the biodiversity assessment, abundance and ac- tivity of organisms (Minster and Connolly, 2006), and novel sequencing technologies (Mardis, 2008) have led to an enormous increase in the amount of genetic data available in the marine communities (Hajibabaei, 2007; Radom et al., 2012; Bik et al., 2012). As a result of this development, the assemblage and analysis of nucleotide data has become routine methodology in most biological disciplines, including marine biodiversity (Karsenti et al., 2011; Teeling and Glockner, 2012; Roger et al., 2012). The molecular tools like genotyping and DNA fingerprinting are being used to study biodiversity in the marine environment. The above said tools, in general, offer the possibility to estimate biodiversity at all levels (e.g. kingdom/class/family/species), in a comparatively small sample size. The general assessment of comparative biodiversity in a larger number of samples were achieved with DNA fingerprinting like DGGE, RAPD, RFLP, SSR, ISSR etc. Further, the phylogenetic analysis of marine organisms was carried out by using marker gene (16S rRNA, 18S rRNA, COI etc.) sequences, and presence or absence of a known spe- cies with species-specific probes using fluorescent in-situ hybridisation (FISH) technique (Mohan et al., 1997). Among these methods, DNA barcoding and meta-barcoding have the potential to increase speed, accuracy and resolution of species iden- tification, while decreasing its cost in biodiversity monitoring (Ji et al., 2013). Besides this, DNA barcoding provides accurate (i.e. avoiding mis-identification) and consistent (level of taxonomic identification e.g. family/genus/species) taxon identification which has proved diffi- cult to achieve traditional morphological approaches. This is particularly true for the large-scale application of macro invertebrate sampling in es- tuary bio-monitoring, where the larval stages are difficult to identify and also species with loss/broken of morphological key character. With respect to genomic analysis, the methodology along with bioinfor- matics tool are being continuously modified and refined in order to serve new purposes and applications in conservation biology and mon- itoring programs (e.g. the projects Fish Poptrace (https://fishpoptrace. jrc.ec.europa) and DEVOTES (http://www.devotes-project.eu). The Marine Pollution Bulletin xxx (2016) xxx–xxx ⁎ Corresponding author. E-mail address: sivabiotech007@gmail.com (S. Sigamani). MPB-07891; No of Pages 7 http://dx.doi.org/10.1016/j.marpolbul.2016.07.017 0025-326X/© 2016 Elsevier Ltd. All rights reserved. Contents lists available at ScienceDirect Marine Pollution Bulletin journal homepage: www.elsevier.com/locate/marpolbul Please cite this article as: Sigamani, S., et al., DNA barcoding of macrofauna act as a tool for assessing marine ecosystem, Marine Pollution Bulletin (2016), http://dx.doi.org/10.1016/j.marpolbul.2016.07.017