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BMC Genomics. 2017 Oct 17;18(1):795. doi: 10.1186/s12864-017-4197-1.

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Author information

Landcare Research, Private Bag, Auckland, 92170, New Zealand.
School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand.
Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Freiburg, Germany.
Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, New Zealand.
School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.
Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-, Martinsried, Germany.
Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
South Australian Museum, North Terrace, GPO Box 234, Adelaide, SA, 5001, Australia.
School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.
Landcare Research, Private Bag, Auckland, 92170, New Zealand.
School of Biological Sciences, The University of Auckland, Auckland, New Zealand.



The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events.


Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes.


The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.


Chemoreceptors; Developmental biology; Epigenetics; Genome assembly; Hexapoda; Horizontal gene transfer; Methylation; Neanuridae; Phylogenomics; RNA; Sex determination

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