An expanded mammal mitogenome dataset from Southeast Asia

Abstract

Southeast (SE) Asia is 1 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 characterized. The growing interest in using environmental DNA 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. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 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. Our new database of 52 taxa will strongly enhance the utility of environmental DNA 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.

The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia

“…The specimen voucher number MZF1072 was deposited in the Zoological Collection of Forest Research Institute Malaysia (FRIM). The methodologies used for DNA isolation, library construction, read assembly, and gene annotation are described in (Mohd Salleh et al 2017;Jahari et al 2020). The mitogenome of R. amplexicaudatus from this study (MT259592) is a circular molecule with 16,511 bp in length.…”

An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies

“…As the costs of HTS decrease, we expect that such gap-filling will increasingly shift towards sequencing of whole mitochondrial genomes of specimen obtained from museum collections, trapping campaigns, etc. [37], reducing the effect of marker choice on detection likelihood. In the meantime, however, the total number of species covered by the database can be increased by combining multiple loci (here, ≤4) and thus the impacts of database gaps on correctly detecting species can be minimized ([60]; Fig.…”

“…For this study, 72 recently published [37] and 7 unpublished partial mitochondrial mammal genomes (accession Nos. MH464789, MH464790, MH464791, MH464792, MH464793, MH464794, MH464795, MH464796, MH464797, MH464798, MH464799, MH464800, MH464801) were added as input (iii).…”

Molecular identification and phylogenetic analysis of aCallosciurus notatuscomplete mitogenome from Peninsular Malaysia

“…When compared against the other mitogenomes available in GenBank, the best BLASTn hit (99.49%) was against a previously sequenced C. notatus (KY117541.1) mitogenome, that also originated in Peninsular Malaysia. In contrast, it differed considerably (92.24% match) to a second C. notatus (KY117542.1) that originated from East Kalimantan, Indonesia (Mohd Salleh et al 2017). This is also clearly mirrored in a phylogenetic analysis showing the relationship of these three mitogenomes with those other Callosciurus species (Figure 1).…”

“…The mitogenome of C. notatus from this study (MT231329) is a circular molecule with 16,582 bp in length. Similar to the mitogenome of other Callosciurus species, it contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (Hu et al 2016;Mohd Salleh et al 2017).…”