De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control.

Arsalan Emami-Khoyi,Shilpa Pradeep Parbhu,Elaine C Murphy,Jennifer Bothwell,Daniela M Monsanto,James G Ross,Peter R Teske,Adrian M Paterson,Bettine Jansen Van Vuuren

doi:10.3390/genes11040436

Arsalan Emami-Khoyi, Shilpa Pradeep Parbhu + Show 7 more

Open Access

https://doi.org/10.3390/genes11040436

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Journal: Genes	Publication Date: Apr 17, 2020
Citations: 8	License type: CC BY 4.0

Affiliation: Lincoln University, University of Johannesburg

Abstract

The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.

Highlights

New Zealand separated from other landmasses approximately 85 million years ago and has remained largely isolated ever since [1]
1 mm3 tissue from liver and brain cerebral cortex were excised, transferred to 10:1 volume of RNAlater solution (Qiagen-Hilden) and stored at −80 ◦ C until RNA was extracted within one week after specimen collection
The histological reports confirmed that three of the brain cerebral cortex biopsies originated from the proximal cortex, while the remainder originated from deeper within the cerebral cortex white matter (Supplementary Materials Figures S1–S4)

Summary

Introduction

New Zealand separated from other landmasses approximately 85 million years ago and has remained largely isolated ever since [1]. By the time the first humans colonised in approximately 1300 AD [2,3], no native land mammals, other than three species of bats, were present [4]. The common brushtail possum (hereafter ‘brushtail possum’) was introduced into New Zealand from localities in Tasmania and the eastern Australian mainland in the 1850s to establish a profitable fur industry [7,8]. The species established itself in the wild, proliferated, and spread across all habitats in the archipelago. In these new habitats, brushtail possums reached population densities far exceeding those in their native Australian range [4]. The scale of devastation upon New Zealand’s endemic ecosystems prompted the brushtail possum’s designation as both an agricultural pest and a major threat to New Zealand’s unique flora and fauna [9,10]

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