Grouper DNA barcoding studies in Indonesia: A short review

1 Master Program in Integrated Coastal Resource Management, Graduate School, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia. 2 Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh 23111, Indonesia. 3 Research Center for Marine and Fisheries Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia.. 4 Laboratory of Genetics and Aquatic Biodiversity, Faculty of Marine and Fisheries, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia. 5Graduate School of Mathematics and Applied Science, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia


Introduction
Indonesia is one region with the highest reef fish biodiversity globally (Allen and Erdmann, 2012). One commercially valuable fish in this area is the groupers (Maulida et al., 2020;Syafei and Sudinno, 2018;Yulianto et al., 2015). At least 76 grouper species have been reported living in Indonesian waters, with three species were categorized into "vulnerable", five species "Data Deficient", and 68 species under the "Least Concern" category based on IUCN classification (IUCN, 2021). The increasing number of exploitations reported caused grouper stocks in Indonesia to decrease and threatened extinction (Fadli et al., 2021;Yulianto et al., 2015). In addition, the use of destructive fishing techniques also affected the fish populations in the wild (Batubara et al., 2017;Muchlisin, 2008;Muchlisin et al., 2015).
Albeit their high economic value in Indonesia, limited scientific information on grouper is available, especially their taxonomy information. In most fish landing sites across Indonesia, the groupers are morphologically identified and recorded as "kerapu" to replace their scientific species names hindering accurate fish recording (Fadli et al., 2021). In addition, morphological identification also required extra accuracy and can lead to misidentification if done without adequate knowledge (Sulistyowatia et al., 2018;Syafei and Sudinno, 2018). Accurate species identification is vital in designing appropriate and sustainable management of fisheries resources (Ardura et al., 2013).
Depik Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan Volume 10, Number 2, Page 186-193 Razi et al. (2021) One of the tools that have been used in fish identification is DNA barcoding. In the last two decades, this molecular method has been employed to identify many fish species globally (Abdullah and Rehbein, 2017;Ali et al., 2020;Bakar et al., 2018;Bamaniya et al., 2016;Bingpeng et al., 2018;Delrieu-Trottin et al., 2019;Duarte et al., 2017;Fadli et al., 2020;Nugroho et al., 2017;Nurilmala et al., 2016;Steinke et al., 2017;Wang et al., 2018;Wibowo et al., 2018) including grouper fish (Alcantara and Yambot, 2016;Basheer et al., 2017;Fadli et al., 2020;Fadli et al., 2021). This method is relatively new in Indonesia, so its use is still limited. It is necessary to conduct a literature review to find out to what extent this approach has been used in Indonesia. Identify which species have been researched, which locations have not been reached, etc., so that the knowledge gaps can be incorporated in future studies. Hence, this study reviewed the DNA barcoding approach in grouper identification in Indonesia based on the available literature.

DNA barcoding
The DNA barcoding technique was introduced in 2003 and has become standardized in molecular taxonomy (Hebert et al., 2003). This approach utilizes a DNA sequence as a taxon 'barcode' of the mitochondrial cytochrome oxidase subunit I gene (COI). There are some advantages of DNA barcoding; (1) DNA barcoding has shown precise discrimination of species groups that have similar morphological shapes (Pavan-Kumar et al., 2018), (2) It can distinguish fish at various developmental phases (Hubert et al., 2010), (3) It can distinguish defective and deficient specimens (Sembiring et al., 2015) and also detect fish in seafood goods (Chin Chin et al., 2016;Marko et al., 2004).
An electronic databank called the Barcode of Life Data System (BOLD; http://www.boldsystems.org/) supports DNA barcoding immense data stored worldwide been created. This web-based catalog permits the acquisition, storage, analysis, and publication of DNA barcode data (Ratnasingham and Hebert, 2007). Over 231,000 animal and 69,000 plant species are documented in BOLD (http://www.boldsystems.org; retrieved on May 7, 2021). Fishes are among the highest barcoded aquatic groups globally, and a project contributed to fishes called The Fish Barcode of Life (FISH-BOL) (http://www.fishbol.org) has been launched (Ward, 2009). A guideline collaborators' set of rules is also accessible to homogenize the data compilation and compliance in the FISH-BOL databank (Steinke and Hanner, 2011). Finally, this approach has developed a progressively vital taxonomic instrument for species recognition and is generally accepted.
The sampling sites for the grouper DNA barcoding studies in Indonesia expanded from Aceh in the western Indonesia region until Papua in the Eastern part of Indonesia. Surprisingly, no sites from Kalimantan Island and limited sampling sites from Northern Sulawesi, Maluku, Southern Papua, etc., were sampled. Epinephelus areolatus was the dominant species found in 13 study sites ( Figure 3, Table 1). Kalimantan, Sulawesi, Maluku, and Papua are in the mid-Indonesia region. This area is the center of the coral triangle and is recognized as the hot spot of tropical marine biodiversity (Veron et al., 2009). Ma et al. (2016), in their research of the historical biogeography of groupers that covered 87% grouper species globally, revealed that the Central Indo-Pacific region (including the mid-Indonesia region) had the highest new grouper species and hypothesized that this region is central to the survival for epinephelids during the Pleistocene epoch. The absence of a sampling site in this area will provide an incomplete picture regarding the genetic pattern of grouper in Indonesia. Various sets of primers were used in these researches, namely Fish F1, Fish R1, Fish F2, Fish R2, AF282, AF283, FH70, RH70, Fish BCL, Fish BCH, 16SAR, 16SBR, Em-01, Em-03, Em-08, Em-07, and Em-10 (Table 2). Research on the Anyperodon genus Ariyanti and Farajallah (2019a) found that mitochondrial COI primers AF282, AF283 have successfully been used to identify the Anyperodon leucogrammicus species. Research on DNA barcoding in the genus Cephalopholis was carried out using different mitochondrial COI primers, including Fish F1, Fish R1 (Ariyanti et al., 2015;Fadli et al., 2021;Fadli et al., 2020); FH70, RH70 (Kamal et al., 2019) Fish BCL, Fish BCH (Andriyono et al., 2020; Andriyono and Suciyono, 2020); 16SAR, 16SBR (Sari et al., 2015); AF282, AF283 (Ariyanti and Farajallah, 2019a) and has been reported to have identified several species in the genus Cephalopholis, namely: C. boenak, C. cyanostigma, C. formosa, C. leopardus, C. miniata, C. nigripinnis, C. sexmaculata, C. sonnerati, C. spiloparaea and C.urodeta. Further research on the genus Cromileptes using primers Fish F1, Fish R1 (Nuryanto et al., 2018); Fish F2, Fish R2 (Susanto et al., 2011;Susanto et al., 2010) have identified the species C. altivelis ( Table 2).

Conclusion
Based on this short literature study, it is indicated that the grouper DNA barcoding research in Indonesia is still limited. Six grouper genera have been barcoded and dominated by the genus Epinephelus (54%). Epinephelus areolatus was the dominant species found in 13 study sites. The sampling sites for the grouper DNA barcoding studies in Indonesia expanded from Aceh in the western Indonesia region until Papua in the Eastern part of Indonesia. However, no sites from Kalimantan Island and limited sampling sites from Northern Sulawesi, Maluku, Southern Papua, etc., were sampled. The research on DNA barcoding needs to be increased to help develop conservation management and sustainable fisheries resource management.