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A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola)

Feng Zhang,Yinhuan Ding,Qing-Song Zhou,Jun Wu,A. Luo,Chaodong Zhu

Published 2019 in Genome Biology and Evolution

ABSTRACT

Abstract Sinella curviseta, among the most widespread springtails (Collembola) in Northern Hemisphere, has often been treated as a model organism in soil ecology and environmental toxicology. However, little information on its genetic knowledge severely hinders our understanding of its adaptations to the soil habitat. We present the largest genome assembly within Collembola using ∼44.86 Gb (118X) of single-molecule real-time Pacific Bioscience Sequel sequencing. The final assembly of 599 scaffolds was ∼381.46 Mb with a N50 length of 3.28 Mb, which captured 95.3% complete and 1.5% partial arthropod Benchmarking Universal Single-Copy Orthologs (n = 1066). Transcripts and circularized mitochondrial genome were also assembled. We predicted 23,943 protein-coding genes, of which 83.88% were supported by transcriptome-based evidence and 82.49% matched protein records in UniProt. In addition, we also identified 222,501 repeats and 881 noncoding RNAs. Phylogenetic reconstructions for Collembola support Tomoceridae sistered to the remaining Entomobryomorpha with the position of Symphypleona not fully resolved. Gene family evolution analyses identified 9,898 gene families, of which 156 experienced significant expansions or contractions. Our high-quality reference genome of S. curviseta provides the genetic basis for future investigations in evolutionary biology, soil ecology, and ecotoxicology.

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