DNA barcoding of lamp shells (Brachiopoda: Lingula anatina) from Probolinggo, East Java, Indonesia
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Abstract. Ambarwati R, Rahayu DA, Rachmadiarti F, Khaleyla F. 2021. DNA barcoding of lamp shells (Brachiopoda: Lingula anatina) from Probolinggo, East Java, Indonesia. Biodiversitas 22: 1764-1774. Lingula anatina is one of brachiopods found in tropical regions, however, the reports on this species from South East Asia is currently limited. This study, therefore, aims to identify the Cytochrome Oxidase subunit I (COI) sequence and phylogenetic of lamp shells from Probolinggo, Indonesia. A total of five samples of lamp shells were collected from Probolinggo, Indonesia, then identified based on morphological characters, and the identification was confirmed using molecular data. Subsequently, molecular characterization and identification were conducted based on 657 bp of COI gene similarity, sequence variation, genetic distance, phylogenetic topology, and BOLD System. According to the results, the Lingula species found in Probolinggo Indonesia was Lingula anatina. The median-joining network and Automatic Barcode Gap Discovery (ABGD) analysis showed this Lingula anatina population from Probolinggo had relatives of 22 haplotypes and divided into six haplogroups. Furthermore, the population belonged to the same haplogroup but had different haplotypes. Thus, this study provides more information for Lingula anatina phylogenetic and haplotype studies.
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References
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Darmarini AS, Wardiatno Y, Prartono T, Soewardi K, 2017. Short communication: New record of primitive brachiopod, Lingula sp. in mangrove ecosystem of Lubuk Damar, Aceh Tamiang, Indonesia. Biodiversitas 18, 1438–1444. https://doi.org/10.13057/biodiv/d180420
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Sahidin A, Zahida Z, Herawati H, Wardiatno Y, Setyobudiandi I, Partasasmita R, 2018. Macrozoobenthos as bioindicator of ecological status in Tanjung Pasir Coastal, Tangerang District, Banten Province, Indonesia. Biodiversitas J. Biol. Divers. 19, 1123–1129. https://doi.org/10.13057/biodiv/d190347
Samanta S, Choudhury A, Chakraborty SK, 2015. Eco-biology of a Precambrian intertidal benthic brachiopod, Lingula anatina from the confluence of Subarnarekha estuary with Bay of Bengal, India. J. Mar. Biol. Ass. India 57, 41–46. https://doi.org/10.6024/jmbai.2015.57.1.1836-06
Samanta S, Choudhury A, Chakraborty SK, 2014. Morpho-anatomical study of Lingula anatina Lamarck, 1801 from West Bengal-Odisha coast, India. J. Mar. Biol. Ass. India 56, 26–33. https://doi.org/10.6024/jmbai.2014.56.2.01775-04
Susanto, A.H., Nuryanto, A., Soedibja, P.H.T., 2012. Phylogeography and Genetic Diversity of Humpback Grouper Cromileptes altivelis based on Cytochrome C Oxidase I. J. Natur Indones. 14, 47–51. https://doi.org/10.31258/jnat.14.1.47-51
Tamura H, 2008. ??. Journal of Chemical Information and Modeling, 53(9), 287. https://doi.org/10.1017/CBO9781107415324.004
Wallace DC, Chalkia D, 2013. Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. Cold Spring Harb. Perspect. Med. 3, 1–47.
Waugh J, Huynen L, Millar C, Lambert D, 2008. DNA barcoding of animal species - Response to DeSalle [1]. BioEssays 30, 92–93. https://doi.org/10.1002/bies.20698
Wibowo A, Farajalah A, Husnah H, 2013. DNA Barcoding of Freshwater Fish Species of Manna River (Bengkulu) And Semanka River (Lampung). Indones. Fish. Res. J. 19, 9. https://doi.org/10.15578/ifrj.19.1.2013.9-17
Ambarwat, R, Rahayu DA, Faizah U, 2019. The Potency and Food Safety of Lamp Shells (Brachiopoda: Lingula sp.) as Food Resources. J. Phys. Conf. Ser. 1417, 12039. https://doi.org/10.1088/1742-6596/1417/1/012039
Anzani L, Madduppa HH, Nurjaya IW, Dias PJ, 2019. Short communication: Molecular identification of white sea squirt Didemnum sp. (tunicata, ascidiacea) colonies growing over corals in raja ampat Islands, Indonesia. Biodiversitas 20, 636–642. https://doi.org/10.13057/biodiv/d200304
Bitner MA, Romanin M, 2018. Recent brachiopods collected during the ZhongSha 2015 expedition to the South China Sea, West Pacific. Mar. Biol. Res. 14, 551–564. https://doi.org/10.1080/17451000.2018.1502447
Darmarini AS, Wardiatno Y, Prartono T, Soewardi K, 2017. Short communication: New record of primitive brachiopod, Lingula sp. in mangrove ecosystem of Lubuk Damar, Aceh Tamiang, Indonesia. Biodiversitas 18, 1438–1444. https://doi.org/10.13057/biodiv/d180420
Emig CC, Bitner MA, Alvarez F, 2013. Phylum Brachiopoda. Zootaxa 3703, 75–78. https://doi.org/10.11646/zootaxa.3703.1.15
Feldman HR, 2017. Tunethyris blodgetti sp. nov. (brachiopoda, terebratulida) from the Middle Triassic of Makhtesh Ramon, Southern Israel. Ann. Soc. Geol. Pol. 87, 89–99. https://doi.org/10.14241/asgp.2017.004
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299. https://doi.org/10.1071/ZO9660275
Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA, 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23, 167–172. https://doi.org/10.1016/j.tig.2007.02.001
Hebert PDN, Gregory TR, 2005. The promise of DNA barcoding for taxonomy. Syst. Biol. 54, 852–859. https://doi.org/10.1080/10635150500354886
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, 2004. Identification of birds through DNA barcodes. PLoS Biol. 2. https://doi.org/10.1371/journal.pbio.0020312
Jackson J, Stiasny G, 1937. The Brachiopoda of the Siboga Expedition. “Siboga Expeditie” XXVII. Leiden.
Jefri E, Zamani NP, Subhan B, Madduppa HH, 2015. Molecular phylogeny inferred from mitochondrial DNA of the grouper epinephelus spp. In Indonesia collected from local fish market. Biodiversitas 16, 254–263. https://doi.org/10.13057/biodiv/d160221
Kenchington R, Hammond L, 1978. Population structure , growth and distribution of Lingula anatina (Brachiopoda) in Queensland, Australia. J. Zool. Lond. 184, 63–81.
Kim SG, Karagozlu MZ, Kim CB, 2017. Phylogenetic investigations of Lingula anatina among some northwestern Pacific populations, based on mitochondrial DNA cytochrome c oxidase subunit I gene. J. Asia-Pacific Biodivers. 10, 162–166. https://doi.org/10.1016/j.japb.2017.04.007
Leopardas V, Honda K, Go GA, Bolisay K, Pantallano AD, Uy W, Fortes M, Nakaoka M, 2016. Variation in macrofaunal communities of sea grass beds along a pollution gradient in Bolinao, northwestern Philippines. Mar. Pollut. Bull. 105, 310–318. https://doi.org/10.1016/j.marpolbul.2016.02.004
Luo YJ, Takeuchi T, Koyanagi R, Yamada L, Kanda M, Khalturina M, Fujie M, Yamasaki SI, Endo K, Satoh N, 2015. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nat. Commun. 6. https://doi.org/10.1038/ncomms9301
Mitra S, Pattanayak JG, 2013. Studies on Lingula anatina (Brachiopoda: Inarticulata) in Subarnarekha Estuary, Odisha with special reference to habitat and population. Rec. Zool. Surv. India 113, 49–53.
Nayak A, Charan KB, Lovaraju A, Raut D, Sanghamitra RS, Dash B, Patnaik L, Mohanty B, Raman A, 2018. Benthic infauna from mudflats of Atharbanki mangrove waterway in Odisha, India. J. Mar. Biol. Assoc. India 60, 33–39. https://doi.org/10.6024/jmbai.2018.60.1.2026-05
Puillandre N, Lambert A, Brouillet S, Achaz G, 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol. Ecol. 21, 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x
Rakmawati, Ambarwati R, 2019. Komunitas Bivalvia yang Berasosiasi dengan Kerang Lentera (Brachiopoda: Lingulata) di Zona Intertidal Selat Madura Bivalves. J. Ris. Biol. dan Apl. 1, 36–42.
Sahidin A, Zahida Z, Herawati H, Wardiatno Y, Setyobudiandi I, Partasasmita R, 2018. Macrozoobenthos as bioindicator of ecological status in Tanjung Pasir Coastal, Tangerang District, Banten Province, Indonesia. Biodiversitas J. Biol. Divers. 19, 1123–1129. https://doi.org/10.13057/biodiv/d190347
Samanta S, Choudhury A, Chakraborty SK, 2015. Eco-biology of a Precambrian intertidal benthic brachiopod, Lingula anatina from the confluence of Subarnarekha estuary with Bay of Bengal, India. J. Mar. Biol. Ass. India 57, 41–46. https://doi.org/10.6024/jmbai.2015.57.1.1836-06
Samanta S, Choudhury A, Chakraborty SK, 2014. Morpho-anatomical study of Lingula anatina Lamarck, 1801 from West Bengal-Odisha coast, India. J. Mar. Biol. Ass. India 56, 26–33. https://doi.org/10.6024/jmbai.2014.56.2.01775-04
Susanto, A.H., Nuryanto, A., Soedibja, P.H.T., 2012. Phylogeography and Genetic Diversity of Humpback Grouper Cromileptes altivelis based on Cytochrome C Oxidase I. J. Natur Indones. 14, 47–51. https://doi.org/10.31258/jnat.14.1.47-51
Tamura H, 2008. ??. Journal of Chemical Information and Modeling, 53(9), 287. https://doi.org/10.1017/CBO9781107415324.004
Wallace DC, Chalkia D, 2013. Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. Cold Spring Harb. Perspect. Med. 3, 1–47.
Waugh J, Huynen L, Millar C, Lambert D, 2008. DNA barcoding of animal species - Response to DeSalle [1]. BioEssays 30, 92–93. https://doi.org/10.1002/bies.20698
Wibowo A, Farajalah A, Husnah H, 2013. DNA Barcoding of Freshwater Fish Species of Manna River (Bengkulu) And Semanka River (Lampung). Indones. Fish. Res. J. 19, 9. https://doi.org/10.15578/ifrj.19.1.2013.9-17
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