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New Insights in Soil Ecology: SMRT Sequencing Powers Genome Assembly of Parthenogenetic Arthropod

Wednesday, September 13, 2017

Photo by Andy Murray

In a recent BMC Genomics paper, scientists in the Netherlands report a high-quality genome assembly for Folsomia candida, a soil-dwelling arthropod. The organism, which is known for reproducing parthenogenetically (and only when infected with Wolbachia), is frequently used in the lab for toxicity testing.

Lead author Anna Faddeeva-Vakhrusheva, senior author Dick Roelofs, and collaborators at Vrije Universiteit Amsterdam and other institutions describe their findings in “Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.” The team chose SMRT Sequencing to characterize the genome so they could learn more about the organism’s reproductive process and stress response.

F. candida has a diploid genome with seven pairs of chromosomes. The scientists generated a 221.7 Mb assembly with a contig N50 of 6.5 Mb. It is remarkably complete, with just 0.1% of all bases marked by gaps. Analysis revealed that repeat segments comprise more than 23% of the genome, and GC content was more than 37%. The team performed a number of quality-control and validation steps, concluding that assembly quality was excellent. The assembly also included the complete 15 kb F. candida mitochondrial genome.

The team was particularly interested in genome content acquired through horizontal gene transfer. A systematic analysis of all genes predicted by the assembly identified more than 800 acquired genes, most of which came from bacteria, fungi, and protists. The complement of horizontally transferred genes was impressive: “This number is among the highest found in metazoan genomes, being only exceeded in rotifers and some nematode species,” the scientists report.

Another highlight of the study came from a focus on F. candida’s endosymbiont Wolbachia. “Parthenogenesis is most likely imposed by Wolbachia,” the team writes. “The presence of Wolbachia is essential for reproduction: animals cured of Wolbachia by antibiotic treatment lay eggs that fail to hatch and develop.” The arthropod sequencing effort also yielded a complete assembly of the endosymbiont, which with its 1.8 Mb genome is the largest strain of Wolbachia ever discovered. Forty-eight genes were found to harbor ankyrin repeats, which are known for “mediating protein-protein and protein-DNA interactions with the host cells,” the scientists note.

Intriguingly, the team identified a functional antibiotic biosynthesis cluster, “suggesting the production of yet undiscovered antimicrobial compounds in an animal genome,” they conclude. “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.”

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