Paper intensive reading (二十七)：High-resolution metatranscriptomics reveals the ecological dynamic...

Title: High-resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia

Author: Mang Shi

7 June 2017

ABSTRACT
Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.

IMPORTANCE Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes.

KEYWORDS: Australia, ecology, evolution, mosquito, phylogeny, transcriptomics, virome

Outline

1.Introduction

2.Results

2.1 The mosquito virome.

2.2 Virome ecology

2.3 Evolutionary history of the newly identified RNA viruses

2.4 Negative-sense RNA viruses

2.5 Positive-sense RNA viruses

2.6 Double-stranded RNA viruses

2.7 Revealing host associations

3.Discussion

4.MATERIALS AND METHODS

4.1 Sample collection

4.2 Sample processing and sequencing

4.3 RNA virus discovery

4.4 Virus genome annotation

4.5 Identification of other microbes within mosquitoes

4.6 RNA quantification

4.7 Phylogenetic analyses

4.8 Accession number(s).

正文摘录

Abstract
    转录组学为了解蚊子RNA病毒提供了重要的观点
     In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.
     转录组学的一个应用
     Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. 

    Discussion
    We have used a metagenomics approach to reveal key aspects of the ecology of RNA viruses in mosquitoes from Western Australia. 
    
    病毒丰度水平是宿主关联的有用指标
    This in turn suggests that the viral abundance level is a useful indicator of host association, although it should be examined in the context of the type and quantity of the dominant microbes within a sample.