Sains Malaysiana 50(4)(2021): 953-965

http://doi.org/10.17576/jsm-2021-5004-07

Mitochondrial Genome of Rattus tiomanicus (Rodentia: Muridae) and Molecular Phylogeny of Murinae

(Genom Mitokondria Rattus tiomanicus (Rodentia: Muridae) dan Filogeni Molekul Murinae)

SZE-LOOI SONG^1,2*, HOI-SEN YONG³, PHAIK-EEM LIM² & JI TAN⁴

¹Institute for Advanced Studies, University of Malaya, 50603 Kuala Lumpur, Federal Territory
Malaysia

²Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia

³Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia

⁴Department of Agricultural and Food Sciences, Universiti Tunku Abdul Rahman, 31900 Kampar, Perak Darul Ridzuan, Malaysia

Received: 26 December 2019/Accepted: 22 September 2020

ABSTRACT

Rattus tiomanicus is a murid rodent of considerable agricultural and public health importance in Southeast Asia. The whole mitochondrial genome of R. tiomanicus was sequenced by the Ion Torrent PGM platform. It had a total length of 16,309 bp, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and two non-coding regions (L-strand replication origin and control region). Only TAA and incomplete T-stop codons were represented in the protein-coding genes. Of the tRNAs, tryptophan (W) had ACU anticodon. The cloverleaf structure for serine S1 (AGN) tRNA lacked the entire D-arm, while in lysine (K) tRNA, the DHU arm lacked the D-loop. Molecular phylogeny based on 15 mt-genes indicated R. tiomanicus having closest genetic affinity to R. rattus complex (R. rattus, R. tanezumi). There were two major clades for the Murinae subfamily namely the Rattini tribe and the Apodemini, Murini and Hydromyini tribes. The whole mitogenome of R. tiomanicus will serve as a useful dataset for studying the systematics and phylogenetic relationships of the murid rodents.

Keywords: Genomics; Murinae; phylogenetics

ABSTRAK

Rattus tiomanicus ialah tikus murid yang penting dalam bidang kesihatan dan pertanian di Asia Tenggara. Seluruh genom mitokondria R. tiomanicus telah dijujuk oleh platfom Ion Torrent PGM. Ia mempunyai jumlah panjang 16,309 bp, terdiri daripada 13 gen yang mengekod protein, dua gen rRNA, 22 gen tRNA dan dua kawasan bukan pengekodan (origin replikasi bebenang L dan kawasan pengawalan). Hanya TAA dan kodon penamat tidak lengkap T berada dalam gen yang mengekod protein. Bagi gen tRNA, triptofan (W) mempunyai antikodon ACU. Struktur kelawar bagi tRNA serina S1 (AGN) kekurangan keseluruhan lengan-D, manakala lengan DHU dalam tRNA lisina (K) kekurangan gelung-D. Filogeni molekul berdasarkan gen-mt 15 menunjukkan R. tiomanicus mempunyai pertalian genetik yang paling dekat dengan R. rattus kompleks (R. rattus, R. tanezumi). Dua klad utama untuk subfamili Murinae adalah untuk suku Rattini dan suku Apodemini, Murini serta Hydromyini. Keseluruhan mitogenom R. tiomanicus adalah bermanfaat untuk memberikan set data dalam mengkaji hubungan sistematik dan filogenetik bagi tikus murid.

Kata kunci: Filogenetik; genom; Murinae

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*Corresponding author; email: szelooi@um.edu.my