An expanded mammal mitogenome dataset from Southeast Asia

• Main Authors: Mohd. Salleh, Faezah, Ramos-Madrigal, Jazmin, Penaloza, Fernando, Liu, Shanlin, Sinding, Mikkel-Holger S., Patel, Riddhi P., Martins, Renata, Lenz, Dorina, Fickel, Joerns, Roos, Christian, Shamsir, Mohd. Shahir, Azman, Mohammad Shahfiz, Lim, Burton K., Rossiter, Stephen J., Wilting, Andreas, Gilbert, M. Thomas P.
• Format: Article
• Language: English
• Published: Oxford Univ Press 2017
• Subjects: TP Chemical technology
• Online Access: http://eprints.utm.my/id/eprint/77355/1/MohdShahirShamsir2017_AnExpandedMammalMitogenomeDataset.pdf; http://eprints.utm.my/id/eprint/77355/

Background: Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterised. The growing interest in using environmental DNA (eDNA) to assess and monitor SE Asian species, in particular threatened mammals - has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion: Our new database of 52 taxa will strongly enhance the utility of eDNA approaches for monitoring mammals in SE Asia, as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database.