De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats

Diana D Moreno-Santillán,Carlos Machain-Williams,Georgina Hernández-Montes,Jorge Ortega

doi:10.1038/s41598-019-42560-9

Abstract

High-throughput RNA sequencing is a powerful tool that allows us to perform gene prediction and analyze tissue-specific overexpression of genes, but also at species level comparisons can be performed, although in a more restricted manner. In the present study complete liver transcriptomes of five tropical bat species were De novo assembled and annotated. Highly expressed genes in the five species were involved in glycolysis and lipid metabolism pathways. Cross-species differential expression analysis was conducted using single copy orthologues shared across the five species. Between 22 and 29 orthologs were upregulated for each species. We detected upregulated expression in Artibeus jamaicensis genes related to fructose metabolism pathway. Such findings can be correlated with A. jamaicensis dietary habits, as it was the unique frugivorous species included. This is the first report of transcriptome assembly by RNA-seq in these species, except for A. jamaicensis and as far as our knowledge is the first cross-species comparisons of transcriptomes and gene expression in tropical bats.

Highlights

The order Chiroptera is the second largest order of mammals and is divided into: two suborders: Yinpterochiroptera and Yangochiroptera[1]
We aim to contribute to the currently available transcriptomic resources for bats by sequencing and assembling the complete liver transcriptomes of five bat species classified into five extant Chiroptera families, namely, Artibeus jamaicensis (Phyllostomidae), Mormoops megalophylla (Mormoopidae), Myotis keaysi (Vespertilionidae), Nyctinomops laticaudatus (Molossidae) and Peropteryx macrotis (Emballonuridae)
In this study we compared the transcriptomes of five species and performed differential expression analysis based only on orthologous transcripts, with the aim of analysing which genes, if any, are upregulated and downregulated in these species and to determine whether this transcript expression can be correlated with the biology of each species, such as dietary habits

Summary

Introduction

The order Chiroptera is the second largest order of mammals and is divided into: two suborders: Yinpterochiroptera and Yangochiroptera[1]. Bats present a wide diversity of feeding habits and may be carnivorous, frugivorous, hematophagous, insectivorous or nectarivorous[2]; as a consequence, chiropters play a crucial roles in the maintenance of the ecosystem balance by providing important ecological services; two-thirds of bats species are insectivorous and as such are considered biological pests controls of agricultural importance[2]. Molecular studies using generation sequencing have made it possible to analyse the whole genome and transcriptome of bats species and have contributed to a better understanding of these evolutionary processes as well as to a new taxonomic classification. We aim to contribute to the currently available transcriptomic resources for bats by sequencing and assembling the complete liver transcriptomes of five bat species classified into five extant Chiroptera families, namely, Artibeus jamaicensis (Phyllostomidae), Mormoops megalophylla (Mormoopidae), Myotis keaysi (Vespertilionidae), Nyctinomops laticaudatus (Molossidae) and Peropteryx macrotis (Emballonuridae). In this study we compared the transcriptomes of five species and performed differential expression analysis based only on orthologous transcripts, with the aim of analysing which genes, if any, are upregulated and downregulated in these species and to determine whether this transcript expression can be correlated with the biology of each species, such as dietary habits

Objectives

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Conclusion