Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life

Abstract

Background: Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor.

Method: We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade.

Results: Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development).

Conclusions: We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.

Fig 1. Phylogenetic relationship among F. candida, O. cincta, L. vannamei, P. monodon, D. pulex, T. castaneum, P. humanus and A. pisum.

The Collembola lineage is represented by F. candida and O. cincta. The Crustacea lineage is represented by two decapods (L. vannamei and P. monodon) and a cladoceran (D. pulex). The Insecta clade is represented by T. castaneum, P. humanusa and A. pisum. The red branches indicate terrestrialization.

Fig 2. Gene Ontology (GO) distribution in F. candida and O. cincta transcriptomes.

The bar chart describes the number of genes assigned to the GO biological processes and molecular functions on level 2 with sequence cut-off of 2 sequences.

Fig 3. Term cloud of over-represented Gene Ontology terms among positively selected genes (PSGs).

(A) GO biological processes over-represented among PSGs in the Hexapoda lineage and (B) in the Collembola lineage. The size of the GO terms is proportional to the p-value obtained in the enrichment test [75], enriched terms were summarized and redundancy was removed with the REVIGO tool [76] using a semantic similarity threshold of 0.7 and D. melanogaster GO Database as reference. The complete dataset of GO enriched terms is presented in the S4 Table.