Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta

PeerJ

article

Kishor Dhaygude¹  Kalevi Trontti²  Jenni Paviala¹  Claire Morandin¹  Christopher Wheat³  Liselotte Sundström¹  Heikki Helanterä¹ 

[1] Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki;Department of Biosciences, Neurogenomics Laboratory, University of Helsinki;Department of Zoology Ecology, Stockholm University;Tvärminne Zoological Station, University of Helsinki

关键词: Pool-seq;    RNA-sequencing;    Ants;    Transcriptome de novo assembly;    Hymenoptera;    Transcriptomics;   

DOI  :  10.7717/peerj.3998

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.

【 授权许可】

CC BY