Abstract
We obtained the complete mitochondrial genome of the Indochinese Forest Rat (Rattus andamanensis). The genome is 16,304 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 control region. The composition and arrangement of genes are analogous to other vertebrates. We used all PCGs to construct phylogenetic tree for R. andamanensis and other 15 Rattus species available on GenBank. The topology indicated that the genus Rattus has two groups and R. andamanensis has a close relationship with R. baluensis, R. tiomanicus, R. rattus, and R. tanezumi.
Rattus andamanensis, which belongs to the genus Rattus, contains 66 species in total and among them 7 species distributed in China (Smith et al. Citation2013). R. andamanensis was previously identified as R. sikkimensis or R. remotus and was mainly distributed in southwestern China and extends to Indo-China, Thailand, Myanmar, and northeastern India (Musser and Carleton Citation2005; Smith et al. Citation2013). There is still controversy about the taxon and distribution of R. andamanensis although there are many studies on genus Rattus (Pages et al. Citation2010; Lu et al. Citation2012; Wei et al. Citation2017). We first sequenced and characterized the complete mitochondrial genome of R. andamanensis to provide more molecular information for this species.
The R. andamanensis specimen (S3565) was collected in August 2018 from Ruyuan, Guangdong Province (25.107°N, 113.265°E), China. The specimen was stored in 95% ethanol and kept in Shandong University (Weihai). Total genomic DNA was isolated from muscle tissue fixed in 95% ethanol using the EasyPure Genomic DNA kit (TransGen Biotech Co., Ltd, Beijing, China). Whole mitochondrial genome was amplified with 13 pairs of primers and sequenced by protocols that were routinely used in our laboratory (Li et al. Citation2019). The resultant sequences were assembled and annotated using the BioEdit 7.2.5 (Hall Citation1999) and MEGA 7.0.14 software (Kumar et al. Citation2016).
The complete mitogenome of R. andamanensis is 16,304 bp in length and has been deposited in GenBank under the accession number MK558274. It contains 37 genes arranged in the same order with other reported vertebrate mitogenomes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. Most genes are transcribed on the heavy (H) strand, except for the nicotinamide adenine dinucleotide dehydrogenase subunit 6 (ND6) and 8 tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser, Glu, Pro) which are transcribed on the light (L) strand. All PCGs start with an ATG codon except ND1 that starts with GTG, DN3 that starts with ATC, ND2, and DN6 that start with ATA. ND1, ND2, COX3 and ND4 end with T and other PCGs end with TAA. All tRNA genes arrange from 60 to 72 bp in length and can be folded into typical clover secondary structure except for tRNA-Ser (AGY) which lacks the dihydrouridine (DHU) arm. The control region is 893 bp in length and locates between tRNA-Pro and tRNA-Phe genes. The overall base composition is 34.0% for A, 12.6% for G, 27.8% for T, and 25.6% for C.
To investigate relationships between R. andamanensis and other Rattus species, we constructed the phylogenetic tree based on 13 PCGs by the ML method using RAxML v7 (Stamatakis, Citation2006) including other 15 Rattus species available on GenBank, and Mus musculus was used as an outgroup. The result showed that the genus Rattus has two groups and R. andamanensis has a sister relationship with R. baluensis, R. tiomanicus, R. rattus and R. tanezumi (). The complete mitochondrial genome of R. andamanensis and phylogenetic analyses will shed light on evolutionary relationships among species in genus Rattus and will be helpful for species delimitation, phylogenetic analysi, and other relative studies.
Figure 1. ML phylogenetic tree of Rattus species based on 13 PCGs under GTR + G + I model. Nodal support was estimated by 1000 bootstrap replicates. ML bootstrap values are shown above nodes.
Acknowledgments
The authors thank the anonymous reviewers for providing valuable comments on the manuscript.
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The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
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References
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