Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida

Abstract

Background Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.ResultsWe applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.ConclusionsThe expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.

At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri

“…Their great abundance, low vagility, long‐term local persistence, and remarkable ecological specificity renders springtails excellent sources of information for inferring biogeographic processes (Garrick, Rowell, Simmons, Hillis, & Sunnucks, ). However, there are both technical and practical limitations to their use for biogeography, including but not restricted to (a) low single‐specimen DNA yields via modern extraction methodologies hinders opportunities for population‐level genomic‐scale analyses; (b) rampant cryptic speciation throughout Class Collembola, renders a priori taxonomic sampling for DNA extraction difficult, if not impossible; (c) limited taxonomic and gene coverage of available reference sequences—genomic datasets have only recently become available for three species (Faddeeva‐Vakhrusheva et al., , ; Wu et al., ); and (d) the dearth of financial resources devoted to springtail research despite their ecological and evolutionary importance. These limitations are reflected in the small molecular datasets (relative to modern genomic standards) and reliance of mitochondrial markers for springtail phylogeography.…”

A massive incorporation of microbial genes into the genome ofTetranychus urticae, a polyphagous arthropod herbivore

“…In contrast to Faddeeva‐Vakhrusheva et al . (), our manual phylogenetic analysis of genes that code for nonribosomal peptide synthases did not point towards an HGT scenario (Supporting Information Table S1). Our phylogenetic reconstructions aligned with other studies that show a wide, albeit sporadic, phylogenetic distribution of nonribosomal peptide synthases, including the Arthropoda and Nematoda phyla (Wang et al ., ).…”

“…In contrast to prokaryotes, the functional impact of an HGT event into an animal recipient on its subsequent evolutionary trajectory generally remains unclear (Crisp et al ., ). Within insects, HGT from microbial genetic sources seems to have been formative in the evolution of many of their phytophagous and detritivorous feeding strategies (Faddeeva‐Vakhrusheva et al ., ; Wybouw et al ., ; Wu et al ., ). Studies in plant‐feeding insects have shown that the enzymatic assimilation of certain plant metabolites is facilitated by the lateral acquisition of microbial genes.…”

Developmental expression and evolution of hexamerin and haemocyanin fromFolsomia candida(Collembola)

“…The combined genomic data for F. candida (DK) from Faddeeva‐Vakhrusheva et al . () and our laboratory (unpublished data) were used as the reference for the transcriptome analyses. The genome index was built using Bowtie2 (Langmead and Salzberg, ), and the reads were mapped using Tophat2 (Kim et al , ).…”