Abstract
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 novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, 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.
Highlights
Phenotypic variation can arise via differences in gene sequences or patterns of gene expression (Carroll, 2008; Simpson, Sword & Lo, 2011)
As the estimated number of the protein coding genes is somewhat smaller in ants than in humans (17,220 genes Oxley et al, 2014) compared to 19,836 in humans (GENCODE release 27, Harrow et al, 2012, and the total genome size much smaller (Tsutsui et al, 2008; Harrow et al, 2012), and our RNA-Seq data was obtained from different life stages and castes, we can expect a reasonably high coverage, missing only transcripts with very low expression levels
In this study we provide insights into essential criteria that should be taken into account for a reliable transcriptome assembly without a reference genome
Summary
Phenotypic variation can arise via differences in gene sequences or patterns of gene expression (Carroll, 2008; Simpson, Sword & Lo, 2011). A diploid, fertilized hymenopteran egg is totipotent, i.e., has the genetic prospects to develop into a queen or a worker, and the developmental trajectory the egg takes among these alternatives is, with a few exceptions (Helms Cahan & Keller, 2003; Pearcy et al, 2004; Fournier et al, 2005), directly influenced by the nutrition and rearing conditions provided by workers (Schwander et al, 2010) These conditions presumably launch a cascade of differential gene expression of a few genes, with large pleiotropic effects at early larval instars causing them to develop into different female castes (Lattorff & Moritz, 2013). Caste determination is controlled by epigenetic mechanisms that are regulated by the social environment, e.g., workers (Gräff et al, 2007; Weil, Korb & Rehli, 2009; Glastad et al, 2011; Zwier et al, 2012; Simola et al, 2013; Simola et al, 2016; Welch & Lister, 2014; Bonasio, 2014; Alvarado et al, 2015; Ashby et al, 2016)
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