Mitochondrial Genome of Endangered Hylobatidae, Hylobates agilis and Hylobates lar, of Peninsular Malaysia

Roberta Chaya Tawie Tingga; Millawati Gani; Badrul Munir Md-Zain

doi:10.55230/mabjournal.v53i3.3047

Authors

Roberta Chaya Tawie Tingga Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia https://orcid.org/0000-0002-6739-656X
Millawati Gani Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia https://orcid.org/0000-0002-9508-7481
Badrul Munir Md-Zain
abgbadd@ukm.edu.my
Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia https://orcid.org/0000-0003-4037-8115

Keywords:

Hylobates agilis, Hylobates lar, mitogenome, next-generation sequencing

Abstract

Hylobates agilis and Hylobates lar, members of the family Hylobatidae, are classified as endangered species in Malaysia due to threats such as population decline and habitat loss. The aim of this study was to sequence and characterize the mitochondrial genome of H. lar and H. agilis. This study reported the total length of mitogenome of H. agilis and H. lar to be 16,473 and 15,949 base pair (bp), respectively. Each sequence contained 13 protein-coding sequences, 2 rRNAs, 22 tRNAs, and a control region D-loop (H. agilis); meanwhile for H. lar, there are 13 protein-coding sequences, 2 rRNAs, 19 trNAs, and a control region D-loop. Phylogenetic analysis showed both species formed a strong monophyletic clade within Hylobates grouping. Mitogenomic data of this study is essential for future references in evolutionary biology and conservation management of endangered Malaysian gibbons in captivity.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

Aifat, N.R. & Md-Zain, B.M. Genetic identification of white-handed gibbons (Hylobates lar) in captivity. 2021. Journal of Sustainability Science and Management, 16(4): 316-326. DOI: https://doi.org/10.46754/jssm.2021.06.023

Baiz, M.D., Tucker, P.K. & Cortés-Ortiz, L. 2018. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Molecular Ecology, 28(5): 1056-1069. DOI: https://doi.org/10.1111/mec.14966

Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313-319. DOI: https://doi.org/10.1016/j.ympev.2012.08.023

Besnard, G., Bertrand J.A.M., Delahaie, B., Bourgeois, Y.X.C., Lhuillier, E. & Thébaud, C. 2016. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biological Journal of the Linnean Society, 117(1): 71-82. DOI: https://doi.org/10.1111/bij.12494

Campbell, C.O., Cheyne, S.M. & Rawson, B.M. 2015. Best practice guidelines for the rehabilitation and translocation of gibbons. International Union for Conservation of Nature, Gland, Switzerland. DOI: https://doi.org/10.2305/IUCN.CH.2015.SSC-OP.51.en

Chan, Y.C., Roos, C., Inoue-Murayama, M., Inoue, E., Shih, C.C., Pei, K.J.C. & Vigilant, L. 2010. Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons. PLoS ONE, 5(12): e14419. DOI: https://doi.org/10.1371/journal.pone.0014419

Chen, L., Lin, Y., Xiao, Q., Lin, Y., Du, Y., Lin, C., Ward-Fear, G., Hu, C., Qu, Y. & Li, H. 2021. Characterization of the complete mitochondrial genome of the many-lined sun skink (Eutropis multifasciata) and comparison with other Scincomorpha species. Genomics, 113(4): 2526-2536. DOI: https://doi.org/10.1016/j.ygeno.2021.05.030

Cortés-Ortiz, L., Roos, C. & Zinner, D. 2019. Introduction to special issue on primate hybridization and hybrid zones. International Journal of Primatology, 40(1): 1-8. DOI: https://doi.org/10.1007/s10764-019-00076-z

Crampton-Platt, A., Timmermans, M.J.T.N., Gimmel, M.L., Kutty, S.N., Cockerill, T.D., Vun Khen, C. & Vogler, A.P. 2015. Soup to tree: The phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Molecular Biology and Evolution, 32(9): 2302-2316. DOI: https://doi.org/10.1093/molbev/msv111

Evanno, G., Regnaut, S. & Goudet, J. 2005. Detecting the number of clusters of individuals using the software structure: A simulation study. Molecular Ecology, 14(8): 2611-2620. DOI: https://doi.org/10.1111/j.1365-294X.2005.02553.x

Finstermeier, K., Zinner, D., Brameier, M., Meyer, M., Kreuz, E., Hofreiter, M. & Roos, C. 2013. A mitogenomic phylogeny of living primates. PLoS ONE, 8(7): e69504. DOI: https://doi.org/10.1371/journal.pone.0069504

Gaur, A., Umapathy, G., Vasudevan, K., Sontakke, S., Rao, S., Goel, S., Kumar, D., Gupta, B., Singh, D.N. & Kumar, A. 2017. Manual for Biological Sample Collection and Preservation for Genetic, Reproductive and Disease Analyses 2017. Central Zoo Authority and LaCONES, New Delhi. 19 pp.

İbiş, O. 2020. Partial mitogenome sequence of the indian crested porcupine (Hystrix indica) in Turkey, with the phylogeny of the subgenus Hystrix. Biology Bulletin, 47(4): 399-406. DOI: https://doi.org/10.1134/S106235902004007X

Kanthaswamy, S., Gill, L., Satkoski, J., Goyal, V., Malladi, V., Kou, A., Kirin Basuta, Sarkisyan, L., George, D. & David Glenn Smith. 2009. Development of a chinese-indian hybrid (chindian) rhesus macaque colony at the California National Primate Research Center by introgression. Journal of Medical Primatology, 38(2): 86-96. DOI: https://doi.org/10.1111/j.1600-0684.2008.00305.x

Kanthaswamy, S., Satkoski, J., George, D.A., Kou, A., Joy, B. & David Glenn Smith. 2008. Hybridization and stratification of nuclear genetic variation in Macaca mulatta and M. fascicularis. International Journal of Primatology, 29(5): 1295-1311. DOI: https://doi.org/10.1007/s10764-008-9295-0

Matsudaira, K. & Ishida, T. 2021. Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. 127(3), 312-322. DOI: https://doi.org/10.1038/s41437-021-00452-7

Matsudaira, K., Reichard, U.H., Ishida, T. & Malaivijitnond, S. 2022. Introgression and mating patterns between white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) in a natural hybrid zone. PLoS ONE, 17(3): e0264519. DOI: https://doi.org/10.1371/journal.pone.0264519

Matsudaira, K., Reichard, U.H., Malaivijitnond, S. & Ishida, T. 2013. Molecular evidence for the introgression between Hylobates lar and H. pileatus in the wild. Primates, 54:33-37. DOI: https://doi.org/10.1007/s10329-012-0323-5

Md-Zain, B.M., Abdul-Latiff, M.A.B, Mohd-Ridwan, A.R. & Najmuddin, M.F. 2022. Primat Semenanjung Malaysia. Jabatan Perhilitan Semenanjung Malaysia, Kuala Lumpur.

Md-Zain, B.M., Mohd-Ridwan, A.R., Muhd-Sahimi, H.N., Abdul-Latiff, M.A.B. & Chan, E. 2021. Mixed-species association among Malaysian primates during the Covid-19 outbreak in Genting Highlands, Peninsular Malaysia. Journal of Sustainability Science and Management, 16(1): 1-10. DOI: https://doi.org/10.46754/jssm.2021.01.001

Mootnick, A.R. 2006. Gibbon (Hylobatidae) species identification recommended for rescue or breeding centers. Primate Conservation, 21: 103-138. DOI: https://doi.org/10.1896/0898-6207.21.1.103

Palombit, R.A. 1995. Longitudinal patterns of reproduction in wild female siamang (Hylobates syndactylus) and white-handed gibbons (Hylobates lar). International Journal of Primatology, 16(5): 739-760. DOI: https://doi.org/10.1007/BF02735718

Roos, C. Phylogeny and classification of gibbons (Hylobatidae). 2016. In: Evolution of gibbons and siamang. Developments in Primatology: Progress and Prospects. U.H. Reichard, H. Hirai and C. Barelli (Eds.). Springer, New York. DOI: https://doi.org/10.1007/978-1-4939-5614-2_7

Tamura, K., Stecher, G. & Kumar, S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7): 022-3027. DOI: https://doi.org/10.1093/molbev/msab120

Thinh, V.N., Mootnick, A.R., Geissmann, T., Li, M., Ziegler, T., Agil, M., Moisson, P., Nadler, T., Walter, L. & Roos, C. 2010. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evolutionary Biology, 10(1): 74. DOI: https://doi.org/10.1186/1471-2148-10-74

Wick, R.R., Judd, L.M., Gorrie, C.L. & Holt, K.E. 2017a. Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomic, 3(10): e000132. DOI: https://doi.org/10.1099/mgen.0.000132

Wick, R.R., Judd, L.M., Gorrie, C.L. & Holt, K.E. 2017b. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology, 13(6): e1005595. DOI: https://doi.org/10.1371/journal.pcbi.1005595

Yimkao, P. & Srikosamatara, S. 2006. Ecology and site-based conservation of the white-handed gibbon (Hylobates lar L.) in human-use forests in Mae Hong Son province, Northern Thailand. Natural History Bulletin of the Siam Society, 54(1): 109-138.