The first complete mitochondrial genome sequence of Cynopterus brachyotis (Chiroptera, Pteropodidae) from the Philippines

Abstract

The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA ofCynopterus brachyotisfrom Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting in a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembledC. brachyotismitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the PhilippineC. brachyotisis only 90%-91% homologous with otherCynopterusspp., based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes, deposited in online repositories, revealed that the PhilippineC. brachyotisin this study has diverged from AsianCynopterus, namelyCynopterus brachyotisandCynopterus sphinxfrom other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the Cynopterus cf. brachyotis in the Philippines is distinct from its Asian counterparts and should be, therefore, treated as a new species.