DNA Barcoding for Identification of Helopeltis sp. from Kaliwining Experimental Station using Mitochondrial COI Gene
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Helopeltis sp. is one of the major pests of the cocoa plant. Helopeltis can decrease cocoa yield by 50 to 60%. Several species of Helopeltis spp. are still often misidentified due to similarity in morphology such as size and color. This study aimed to identify Helopeltis sp. through DNA barcoding using the mitochondrial cyto- chrome C oxidase subunit 1 (COI) gene. Analysis was carried out on 100 adults Helopeltis sp. from Kaliwining Experimental Station, Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia. Specimens were preserved in 96% ethyl alcohol at 4oC until molecular studies were carried out. PCR amplification was conducted through specific primer from COI gene. Sequences data analysis using MEGA 5.05 software was carried out. The study results using DNA barcoding showed that Helopeltis samples in Kaliwining cocoa plantations are Helopeltis bradyi with a percentage identity above 99% and E value of 0; this sequence as significantly matched. Mean length of the sequences was 679.5 base pairs. Phy- logenetic tree data also shows that the Helopeltis species analysed were also of the same descent, H. bradyi with the accession number KT189562.1. Helopeltis sp. specimens were clustered together. No taxonomic deviation was detected at the species level, indicating that most of the examined species of Helopeltis sp. could be authenticated by the barcode approach using the COI gene. In addi- tion, Helopeltis specimens were also aligned with H. antonii and H. theivora from the genebank to determine their genetic relationship.
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Dec 30, 2022
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Abstract
Helopeltis sp. is one of the major pests of the cocoa plant. Helopeltis can decrease cocoa yield by 50 to 60%. Several species of Helopeltis spp. are still often misidentified due to similarity in morphology such as size and color. This study aimed to identify Helopeltis sp. through DNA barcoding using the mitochondrial cyto- chrome C oxidase subunit 1 (COI) gene. Analysis was carried out on 100 adults Helopeltis sp. from Kaliwining Experimental Station, Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia. Specimens were preserved in 96% ethyl alcohol at 4oC until molecular studies were carried out. PCR amplification was conducted through specific primer from COI gene. Sequences data analysis using MEGA 5.05 software was carried out. The study results using DNA barcoding showed that Helopeltis samples in Kaliwining cocoa plantations are Helopeltis bradyi with a percentage identity above 99% and E value of 0; this sequence as significantly matched. Mean length of the sequences was 679.5 base pairs. Phy- logenetic tree data also shows that the Helopeltis species analysed were also of the same descent, H. bradyi with the accession number KT189562.1. Helopeltis sp. specimens were clustered together. No taxonomic deviation was detected at the species level, indicating that most of the examined species of Helopeltis sp. could be authenticated by the barcode approach using the COI gene. In addi- tion, Helopeltis specimens were also aligned with H. antonii and H. theivora from the genebank to determine their genetic relationship.
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Pancaningtyas, S., Tunjung Sari, A., & Rahayu, D. (2022). DNA Barcoding for Identification of Helopeltis sp. from Kaliwining Experimental Station using Mitochondrial COI Gene. Pelita Perkebunan (a Coffee and Cocoa Research Journal), 38(3), 179-189. https://doi.org/10.22302/iccri.jur.pelitaperkebunan.v38i3.521
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References
Asokan, R.; K.B. Rebijith; K.K. Srikumar; P. Shivarama Bhat; V.V. Ramamurthy (2012). Molecular Identification and Diversity of Helopeltis antonii and Helopeltis theivora (Hemiptera: Miridae) in India. Florida entomologist, 95(2), 350-358.
Carol, D.; von Dohlen; A. Nancy; Moran (2000). Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation, Biological Journal of the Linnean Society, 71(4), 689–717, https://doi.org/10.1111/j.1095-8312.2000.tb01286.x
Cempaka, Gita. 2015. Identifikasi Jenis Dan Inang Kepik Helopeltis Didaerah Bogor Dan Cianjur. Fakultas Pertanian, Institut Pertanian Bogor. Bogor.
Filipova L, F. Grandjean; D.A. Lieb; A. Petrusek (2011). Haplotype variation in the spiny-cheek crayfish Orconecteslimosus: colonization of Europe and genetic diversity of native stocks. Journal of the North American Benthological Society, 30:871–881.
Henry, T.; P.C. Iwen; S.H. Hinrichs (2000). Identification of Aspergillus Species using Internal Transcribed Spacer Region 1 and 2. Journal of Clinical Microbiology, 38(4), 1510-5. DOI: https://doi.org/10.1128/JCM.38.4.1510-1515.2000
Huang, Z.; R. Ruan (2017). DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes). Mitochondrial DNA A DNA Mapp Seq Anal. 29(4), 529-534. doi: 10.1080/24701394.2017.1315569
Jalali, S.; R. Ojha; T. Venkatesan (2015). DNA Barcoding for Identification of Agriculturally Important Insects. In: Chakravarthy, A. (eds) New Horizons in Insect Science: Towards Sustainable Pest Management. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2089-3_2
Ji, Y.J.; D.X. Zhang; L. He (2003). Evolutionary conservation and versatility of new set of primers for amplifying the ribosomal transcribed spacer regions in insects and other invertebrates. Molecular Ecology Notes, 3, 581-585
Kn, Chandrashekara; R. Kumar; V. Kumar; D. Banerjee; S. Kundu; B. Ghosh; K. Tyagi (2015). DNA barcoding reveals host-associated genetic diversity of ‘tea mosquito bug’ Helopeltis theivora (Miridae: Heteroptera) from India. Journal of Asia-Pacific Entomology, 18, 541–545. 10.1016/j.aspen.2015.07.004.
Latip; R. Muhamad; M. Gnanasegaram; S. Tan (2010). Development of microsatellite markers for Helopeltis theivora Waterhouse (Hemiptera: Miridae). African Journal of Biotechnology, 9, 4478-4481.
Madden, M.J.L.; R.G. Young; J.W. Brown; S.E. Miller; A.J. Frewin; R.H. Manner (2019). Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry. PLOS ONE, 14(9), e0222291
Melina, S., E. Martono, Y.A. Trisyono.2016. Confirmation that Helopeltis species attacking cacao in Yogyakarta is Helopeltis bradyi Waterhouse, not Helopeltis antonii Signoret (Heteroptera: Miridae). Indonesian Journal of Entomology, 13(1), 9-20.
Palraju, M.; R. Paulchamy; S. Sundaraman (2018). Population genetic structure and molecular diversity of Leucinodesorbonalis based on mitochondrial COI gene sequences. Mitochondrial DNA, 29, 1231–1239.
Rebijith, K. B., Asokan, R., Krishna, V., Kumar, N. K. K., & Ramamurthy, V. V. (2012). Development of Species-Specific Markers and Molecular Differences In Mitochondrial And Nuclear DNA Sequences of Aphis gossypii and Myzus persicae (Hemiptera: Aphididae). The Florida Entomologist, 95(3), 674–682. http://www.jstor.org/stable/23268491
Rubinoff, D., Cameron, S. & Will, K. (2006) A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. Journal of Heredity, 97, 581– 594.
Signoret, V. (1858). Description de Nouvelles espèces d’Hémiptères. II. Note sur les Hémiptères Héteroptères de la famille des unicellules. Annales de la Société Entomologique de France, 3, 499-502
Stonedahl, G. M. (1991). The Oriental Species of Helopeltis (Heteroptera: Miridae): a Review of Economic Literatur And Guide to Identification. Bulletin of Entomological Research 81: 465-490
Sulistyowati, E.; M. Ghorir; S. Wardani; S. Purwoko (2014). Keefektifan serai, bawang merah, dan bunga paitan sebagai insektisida nabati terhadap penghisap buah kakao, Helopeltis antonii. Pelita Perkebunan, 30(1), 35-46.
Sulistyowati, E. (2015). Hama Utama Tanaman Kakao dan Pengendaliannya, bagian dari buku KAKAO : Sejarah, Botani, Proses Produksi, Pengolahan dan Perdagangan. Gadjah Mada University Press. Yogyakarta. 728 p.
Von Dohlen, C.D. (2000). Molecular data support a rapid radiation of aphids in Cretaceous and multiple origins of host alternation. Biological Journal of the Linnaean Society, 71, 689-717
Xu, Z.H.; J.L. Chen; D.F. Cheng; Y. Liu; F. Frederic (2011). Genetic variation among the geographic population of the Grain Aphid, Sitobiona venae (Hemiptera: Aphididae) in China inferred from the mitochondrial COI gene sequence. Agricultural Science in China, 10, 1041–1048.
Carol, D.; von Dohlen; A. Nancy; Moran (2000). Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation, Biological Journal of the Linnean Society, 71(4), 689–717, https://doi.org/10.1111/j.1095-8312.2000.tb01286.x
Cempaka, Gita. 2015. Identifikasi Jenis Dan Inang Kepik Helopeltis Didaerah Bogor Dan Cianjur. Fakultas Pertanian, Institut Pertanian Bogor. Bogor.
Filipova L, F. Grandjean; D.A. Lieb; A. Petrusek (2011). Haplotype variation in the spiny-cheek crayfish Orconecteslimosus: colonization of Europe and genetic diversity of native stocks. Journal of the North American Benthological Society, 30:871–881.
Henry, T.; P.C. Iwen; S.H. Hinrichs (2000). Identification of Aspergillus Species using Internal Transcribed Spacer Region 1 and 2. Journal of Clinical Microbiology, 38(4), 1510-5. DOI: https://doi.org/10.1128/JCM.38.4.1510-1515.2000
Huang, Z.; R. Ruan (2017). DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes). Mitochondrial DNA A DNA Mapp Seq Anal. 29(4), 529-534. doi: 10.1080/24701394.2017.1315569
Jalali, S.; R. Ojha; T. Venkatesan (2015). DNA Barcoding for Identification of Agriculturally Important Insects. In: Chakravarthy, A. (eds) New Horizons in Insect Science: Towards Sustainable Pest Management. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2089-3_2
Ji, Y.J.; D.X. Zhang; L. He (2003). Evolutionary conservation and versatility of new set of primers for amplifying the ribosomal transcribed spacer regions in insects and other invertebrates. Molecular Ecology Notes, 3, 581-585
Kn, Chandrashekara; R. Kumar; V. Kumar; D. Banerjee; S. Kundu; B. Ghosh; K. Tyagi (2015). DNA barcoding reveals host-associated genetic diversity of ‘tea mosquito bug’ Helopeltis theivora (Miridae: Heteroptera) from India. Journal of Asia-Pacific Entomology, 18, 541–545. 10.1016/j.aspen.2015.07.004.
Latip; R. Muhamad; M. Gnanasegaram; S. Tan (2010). Development of microsatellite markers for Helopeltis theivora Waterhouse (Hemiptera: Miridae). African Journal of Biotechnology, 9, 4478-4481.
Madden, M.J.L.; R.G. Young; J.W. Brown; S.E. Miller; A.J. Frewin; R.H. Manner (2019). Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry. PLOS ONE, 14(9), e0222291
Melina, S., E. Martono, Y.A. Trisyono.2016. Confirmation that Helopeltis species attacking cacao in Yogyakarta is Helopeltis bradyi Waterhouse, not Helopeltis antonii Signoret (Heteroptera: Miridae). Indonesian Journal of Entomology, 13(1), 9-20.
Palraju, M.; R. Paulchamy; S. Sundaraman (2018). Population genetic structure and molecular diversity of Leucinodesorbonalis based on mitochondrial COI gene sequences. Mitochondrial DNA, 29, 1231–1239.
Rebijith, K. B., Asokan, R., Krishna, V., Kumar, N. K. K., & Ramamurthy, V. V. (2012). Development of Species-Specific Markers and Molecular Differences In Mitochondrial And Nuclear DNA Sequences of Aphis gossypii and Myzus persicae (Hemiptera: Aphididae). The Florida Entomologist, 95(3), 674–682. http://www.jstor.org/stable/23268491
Rubinoff, D., Cameron, S. & Will, K. (2006) A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. Journal of Heredity, 97, 581– 594.
Signoret, V. (1858). Description de Nouvelles espèces d’Hémiptères. II. Note sur les Hémiptères Héteroptères de la famille des unicellules. Annales de la Société Entomologique de France, 3, 499-502
Stonedahl, G. M. (1991). The Oriental Species of Helopeltis (Heteroptera: Miridae): a Review of Economic Literatur And Guide to Identification. Bulletin of Entomological Research 81: 465-490
Sulistyowati, E.; M. Ghorir; S. Wardani; S. Purwoko (2014). Keefektifan serai, bawang merah, dan bunga paitan sebagai insektisida nabati terhadap penghisap buah kakao, Helopeltis antonii. Pelita Perkebunan, 30(1), 35-46.
Sulistyowati, E. (2015). Hama Utama Tanaman Kakao dan Pengendaliannya, bagian dari buku KAKAO : Sejarah, Botani, Proses Produksi, Pengolahan dan Perdagangan. Gadjah Mada University Press. Yogyakarta. 728 p.
Von Dohlen, C.D. (2000). Molecular data support a rapid radiation of aphids in Cretaceous and multiple origins of host alternation. Biological Journal of the Linnaean Society, 71, 689-717
Xu, Z.H.; J.L. Chen; D.F. Cheng; Y. Liu; F. Frederic (2011). Genetic variation among the geographic population of the Grain Aphid, Sitobiona venae (Hemiptera: Aphididae) in China inferred from the mitochondrial COI gene sequence. Agricultural Science in China, 10, 1041–1048.
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