Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing

Abstract

Background: In the past two decades, bats have emerged as an important model system to study host-pathogen interactions. More recently, it has been shown that bats may also serve as a new and excellent model to study aging, inflammation, and cancer, among other important biological processes. The cave nectar bat or lesser dawn bat (Eonycteris spelaea) is known to be a reservoir for several viruses and intracellular bacteria. It is widely distributed throughout the tropics and subtropics from India to Southeast Asia and pollinates several plant species, including the culturally and economically important durian in the region. Here, we report the whole-genome and transcriptome sequencing, followed by subsequent de novo assembly, of the E. spelaea genome solely using the Pacific Biosciences (PacBio) long-read sequencing platform.

Findings: The newly assembled E. spelaea genome is 1.97 Gb in length and consists of 4,470 sequences with a contig N50 of 8.0 Mb. Identified repeat elements covered 34.65% of the genome, and 20,640 unique protein-coding genes with 39,526 transcripts were annotated.

Conclusions: We demonstrated that the PacBio long-read sequencing platform alone is sufficient to generate a comprehensive de novo assembled genome and transcriptome of an important bat species. These results will provide useful insights and act as a resource to expand our understanding of bat evolution, ecology, physiology, immunology, viral infection, and transmission dynamics.

Figure 1:

Female cave nectar bat (Eonycteris spelaea) with pup.

Figure 2:

Venn diagram for coding gene predictions based on evidence sources. The different colors indicate various sources of evidence, and the values reflect the number of genes supported by each type of evidence.

Figure 3:

Maximum-likelihood phylogenetic analysis of 3,185 genes in bats and mammalian species. The estimated divergence time (100 Mya) is given at the nodes, with the 95% confidence intervals in parentheses. Monodelphis domestica, used as an outgroup species, was excluded in this figure.

Figure 4:

The alternative splicing of E. spelaea’s coding genes. (A) Comparison of number of alternative transcripts per annotated gene between H. sapiens, P. alecto, E. spelaea, and PacBio Iso-Seq E. spelaea transcriptomes. (B) Comparison of rate of occurrence for the different classes of alternative transcripts between H. sapiens, P. alecto, and the E. spelaea PacBio Iso-Seq transcriptome. Abbreviations: A5/A3: alternative 5′/3′ splice sites; AF/AL: alternative first/last exons; MX: mutually exclusive exons; RI: retained intron; SE: skipping exon.