Genetic Characteristics of Chloropsis cochinchinensis Gmelin, 1789 Based on The Mitochondrial DNA COI Gene


Jarulis Jarulis(1*), Apin Saputra(2), Risky Hadi Wibowo(3)

(1) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Bengkulu, Indonesia, 38371, Indonesia
(2) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Bengkulu, Indonesia, 38371, Indonesia
(3) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Bengkulu, Indonesia, 38371, Indonesia
(*) Corresponding Author

Abstract


The rate of illegal poaching of blue-winged leafbirds (Chloropsis cochinchinensis) throughout Indonesia, particularly Bengkulu, is quite high. However, only minimal molecular information is available for this species. We performed mtDNA COI gene sequencing to explore genetic characters (conservative site, variable site, parsimony site, and singleton site) of blue-winged leafbirds. Using Qiagen's DNeasy® Blood and Tissue Kit based on the Spin-Column Protocol, total DNA was isolated, and PCR amplification methods were performed. DNA derived from a PCR reaction was forwarded to PT. First Base Malaysia for sequencing. Using MEGA 10.0 and BIOEDIT, the COI gene nucleotide sequence data were assembled, edited, and analyzed to explore of single nucleotide polymorphism, genetic distance, and phylogeny. The 616 bp COI genes contained 566 conservative sites (C), 50 variation sites (V), 24 information parsimony sites (Pi), and 26 singleton sites (S), as indicated by the results. The greatest nucleotide base composition was cytosine (34.1–34.9%), while the lowest was guanine (15.7–16.2%). The proportion of adenine-thymine nucleotide base pairs was greater than that of guanine-cytosine (50.3%). There were 26 barcode-specific mutation sites, 17 transition substitution mutation sites, and 9 transverse substitution mutation sites. The average genetic distance between C. cochinchinensis individuals was 2.2%, but the average genetic difference between species was 9.0%. All C. cochinchinensis individuals in our sample clustered within the same clade and were distinguished from other species within the same genus. The COI gene sequences of C. cochinchinensis that we acquired are novel and can be utilized for molecular identification of the species.


Keywords


barcode, Chloropseidae, conservation, mitochondrial, phylogeny, poaching

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References


Arif, I. A., Khan, H. A., Shobrak, M. & Williams J. (2011). Cytochrome C Oxidase Subunit I Barcoding of the Green Bee-eater (Merops orientalis). Genet Mol Res, 10, 3992-3998. DOI: 10.4238/2011.October.21.2.

Astuti, D. & Sulandari, S. (2010). The DNA Sequence Performance of COI Gene in White Cockatoos (Cacatua, Psittacifrmes). Treubia, 37, 1-14.

Astuti, D., Ashari, H., Irham, M., & Sulandari, S. (2017). Analysis of the Cytochrome Oxydase-1 (COI) Gene to Confirm The Taxonomy Status of Sumbawa Drongo (Dicrurus, Dicruridae). Zoo Indonesia, 26(1), 44-51. DOI: 10.52508/zi.v26i1.3534.

Astuti, D. & Prijono, S. N. (2018). Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene. Biosaintifika: Journal of Biology & Biology Education, 10(2), 465-471. DOI: 10.15294/biosaintifika.v10i2. 13501.

Bangkulu, T., Mege, R. A. & Mokosuli, Y. S. (2020). Barcoding Molekuler Burung Nuri Talaud Berdasarkan Gen COI (Cytochrome Oxidase Subunit I). Jurnal Nukleus Biosains, 1(1), 21-25.

Cai, Y., Yue, B., Jiang, W., Xie, S., Li, J. & Zhou, M. (2010). DNA Barcoding on Subsets of Three Families in Aves. Mitochondrial DNA, 21(3-4), 132-137. DOI: 10.3109/ 19401736.2010.494726.

Dharmayanti, N. L. P. I. (2011). Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution history. Wartazoa, 21, 1-10.

Dor, R., Safran, R. J., Sheldon, F. H., Winkler, D. W. & Lovette, I. J. (2010). Phylogeny of the genus Hirundo and the Barn Swallow Subspecies Complex. Molecular Phylogenetics and Evolution, Elsevier Inc., 56(1), 409-418. DOI: 10.1016/j.ympev.2010.02.008.

Efe, M. A., Tavares, E. S., Baker, A. J. & Bonatto, S. L. (2009). Multigene Phylogeny and DNA Barcoding Indicate That The Sandwich Tern Complex (Thalasseus sandvicensis, Laridae, Sternini) Comprises Two Species. Molecular Phylogenetics and Evolution, Elsevier Inc., 52(1), 263–267. DOI:10.1016/j.ympev.2009.03.030.

Hall, T. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98NT. Nucleic Acids Symposium Series, 41, 95-98.

Hunt, J. S., Bermingham, E. & Ricklefs, R. E. (2001). Molecular Systematics and Biogeography of Antillean Thrashers, Tremblers, and Mockingbirds (Aves: Mimidae). The Auk, 118(1), 35–55.

Hebert, P. D. N., Cywinska, A., Ball, S. L. & Waard, J. R. de. (2003a). Biological Identifications Through DNA Barcodes. Proceeding of the Royal Society London, 270, 313−321. DOI: 10.1098/rspb.2002.2218.

Hebert, P. D. N., Ratnasingham, S. & Waard, J. R. de. (2003b). Barcoding Animal Life : Cytochrome C Oxidase Subunit 1 Divergences Among Closely Related Species. Proceeding of The Royal Society Lond. B, 270, 96-99. DOI: 10.1098/rsbl.2003.0025.

Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. (2004). Ten Species in One: DNA Barcoding Reveals Cryptic Species in the Neotropical Skipper Butterfly Astraptes Fulgerator. Proceedings of The National Academy of Sciences of The United States of America, 101(41), 14812-14817. DOI: 10.1073/pnas.0406166101.

Huang, Z. & Tu, F. (2016). DNA Barcoding and Phylogeny of Calidris and Tringa (Aves: Scolopacidae). Mitochondrial DNA Part A, 28(4), 616-619. DOI: 10.3109/ 24701394.2016.1155121.

Iskandar, J. & Iskandar, B. S. (2020). The Effect of the Partial Solar Eclipseon Behavior of Three Species of Ardeidae Rancabayawak Bandung. Jurnal Biodjati, 5(2), 316-328. DOI: 10.15575/ biodjati.v5i2.4578.

IUCN. (2019). Blue-winged leafbird Chloropsis cocinchinensis. The IUCN Red List of Threatened Species 2019. Bird Life International.

Johnsen, A., Rindal, E., Ericson, P. G. P., Zuccon, D., Kerr., K. C. R., Stoeckle., M. Y., & Lifjeld, J. T. (2010). DNA Barcoding of Scandinavian Birds Reveals Divergent Lineages in Trans-Atlantic Species. Journal of Ornithology, 151(3), 565–578. DOI: 10.1007/s10336-009-0490-3.

Jarulis., Solihin, D. D., Mardiastuti, A. & Prasetyo, L. B. (2018). DNA Barcode of Seven Indonesian Hornbills Species (Aves: Bucerotidae) Based on Mitochondrial DNA Cytochrome Oxidase Subunit I. Hayati Journal of Biosciences, 25(4), 178–187. DOI: 10.4308/hjb.25.4.178.

Jarulis., Muslim, C., Kamilah, S. N., Utama, A. F., Permana, D., Sari, M. M., Prayitno, A. H. & Jannah, I. M. (2021). DNA Barcode of Enggano hill myna, Gracula religiosa enganensis (Aves: Sturnidae) Based on Mitochondrial DNA Cytochrome Oxidase Subunit I. Biodiversitas, 22(4), 1635-1643. DOI: 10.13057/biodiv/d220407.

Jarulis, Nurmeiliasari, Haryanto, H. & Vilanda, I. (2022). DNA Barcode of Red Junglefowl Gallus gallus L, 1958 (Aves: Phasianidae) of Sumatra Based on Mitochondrial COI DNA Gene. Biosaintifika, 14(2), 200-210. DOI: 10.15294/biosaintifika.v14i2.36530.

Juhardiansyah, Erianto, H. & Idam H. M. (2019). Studi Jenis Burung yang Diperdagangkan di Kota Ketapang. Jurnal Hutan Lestari, 7(1), 237-247.

Kementerian Lingkungan Hidup dan Kehutanan. (2018). Peraturan Menteri Lingkungan Hidup dan Kehutanan Republik Indonesia Nomor P.106/MENLHK/SETJEN/KUM.1/12/2018 Tentang Jenis Tumbuhan dan Satwa Yang Dilindungi. Jakarta.

Kimura, M. (1980). A Simple Method for Estimating Evolutionary Rates of Base Substitutions Through Comparative Studies of Nucleotide Sequences. Journal of Molecular Evolution, 16, 111-120.

Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis Across Computing Platforms. Molecular Biology and Evolution, 35,1547-1549. DOI: 10.1093/molbev/msy096.

Lim, H. C., Saucier, J., Milensky, C., & Mulcahy, D. G. (2018). Improving collections of Borneo Forest Avifauna. Retrived from https://www.ncbi.nlm.nih.gov/nuccore/MH929123.1.

Mackinnon, J., Phillipps, K. & Balen, bas, V. (2010). Burung-Burung di Sumatera, Jawa, Bali dan Kalimantan. Bogor: Lembaga Ilmu Pengetahuan Indonesia.

Mafaja, K. & Husain, F. (2019). Kelompok Kicau Mania, Kontes Burung dan Kesadaran Konservasi Burung Kicau Di Kabupaten Blora. Solidarity, 8(1), 602-613.

Moltesen, M., Irestedt, M., Fjeldså, J., Ericson, Per. G. P., Jønsson, & Knud J. (2012). Molecular phylogeny of Chloropseidae and Irenidae-Cryptic species and biogeography. Molecular Phylogenetics and Evolution, 65, 903-914. DOI: 10.1016/ j.ympev.2012. 08.012.

Osawa, S., Su, Z. H. & Imura, Y. (2004). Molecular Phylogeny and Evolution of Carabid Ground beetles. Tokyo: Springer Verlag.

Pradita, D. (2018). Mitologi sampai Perdagangan: Status, Peran, dan Makna Burung dalam Masyarakat Jawa dari Zaman Kolonial sampai Milenial. Prosiding Konferensi Peneliti dan Pemerhati Burung Indonesia (KPPBI) 4, 388-402. Semarang.

Rahayu, A. R., Kusumaningrum, H. P. & Budiharjo, A. (2016). Pelacakan Gen Sitokrom Oksidase Subunit 1 (CO1) DNA Mitokondria pada Itik Tegal (Anas sp.). BIOMA, 18(2), 114-122.

Susanto, M. H., Angga P. N. & Marwa, M. H. M. 2021. Jual-Beli Satwa Burung Dilindungi Negara: Tinjauan Hukum Perjanjian dan Penegakan Hukumnya. Res Judicata, 4(2), 133-149.

Susanti, R., Iswari, R. S., Fibriana, F. & Indriawati. (2018). The Duck Cytochrome Oxidase I (COI) Gene: Sequence and Patterns Analysis for Potential Barcoding tool. Biodiversitas, 19(3), 997-1003. DOI: 10.13057/biodiv/d190331.

Sutarno, S. (2003). Genetic Diversity: Detection of Gene Variation at the DNA Level and Utilization of Gene Markers on Locating Qtls. Biodiversitas, Journal of Biological Diversity, 4(1), 58–62. DOI: 10.13057/biodiv/d040112.

Vilaça, S. T., Lacerda, D. R., Sari., E. H. R. & Santos, F. R. (2006). DNA-Based Identification Applied to Thamnophilidae (Passeriformes) Species: The First Barcodes of Neotropical Birds. Revista Brasileira De Ornitologia, 14(1), 7–13.

Waugh, J. (2007). DNA Barcoding in Animal Species: Progress, Potential and Pitfalls. Bioessays, 29(2), 188–197. DOI: 10.1002/bies.20529.

Whittier, J. B., Leslie, D. M. & Bussche, V. D. R. A. (2006). Genetic Variation Among Subspecies of Least Tern (Sterna antillarum): Implications for Conservation. Waterbirds, 29(2), 176–184.

Zein, M. S. A. (2018). Barkoding DNA Burung Elang (Famili Accipitridae) di Indonesia. Jurnal Ilmu-ilmu Hayati, 17(2), 165-73. DOI: 10.14203/beritabiologi.v17i2.3108.




DOI: https://doi.org/10.15575/biodjati.v8i1.20260

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