December 28, 2017  |  Plant + animal biology

New nematode assembly simplifies search for evolutionary clues

Nematodes are both simple and complex, making them one of the most attractive animal taxa to study basic biological processes, including genome evolution. Studies in the nematode Caenorhabditis elegans, for instance, have provided invaluable insights into almost all aspects of biology, from developmental to neurobiology and human diseases.

However, the high degree of fragmentation of current genome assemblies for many organisms complicates almost all types of genomic analysis. As the authors of a recent Cell Reports paper, Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus, point out, “general questions of chromosome evolution cannot be addressed if genome assemblies consist of thousands of contigs.”

SMRT Sequencing was able to remedy this problem. By sequencing the genome of P. pacificus with the PacBio Sequel System, Christian Roedelsperger, Ralf J. Sommer, and other colleagues from the Max Planck Institute for Developmental Biology generated an assembly that reduced the number of contigs from 12,395 to 135 and simplified their search for clues into developmental systems drift, the genetics of phenotypic plasticity, and genome evolution.

pacificus has become an increasingly important model species, used in comparison to two other free-living nematode species, C. elegans and C. briggsae, to investigate how various biological pathways and their underlying regulatory programs are modified during evolution.

Populated primarily by self-fertilizing hermaphrodites with a low frequency of males, all three species undergo frequent recombination among different genetic lineages. Their genomes range in size from 100-160 Mb, but all have five autosomes and one sex chromosome. Many of their shared features are controlled by completely different molecular programs, a phenomenon referred to as ‘‘developmental systems drift,” making them particularly useful in comparative biology.
pacificus is also one of the most promising animal models in the investigation of “phenotypic plasticity,” the property of a single genotype to form distinct phenotypes in response to different environmental influences. In P. pacificus, for instance, young nematode larvae either develop directly into adults or into non-feeding, long-lived dauer larvae, which can disperse to find more suitable environments. They also exhibit two different mouth morphs that are specialized for either bacterial or predatory feeding.

For these reasons, the Max Planck team was particularly interested in unravelling some of their genetic mysteries. They sequenced the genome of the P. pacificus reference strain (PS312) on the Sequel System to 100-fold coverage. The resulting de novo assembly enabled ordering and orientation of contigs for all six P. pacificus chromosomes. “This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny,” the authors write.

Among their findings was the discovery of a major translocation from autosomes to the sex chromosome during the evolution of the lineage leading to C. elegans.“These findings highlight the impact of large-scale chromosomal rearrangements in nematode genome evolution and emphasize the need for high-quality genome assemblies to robustly study these events,” add the authors. “The new P. pacificus assembly will allow more rigorous genomewide analysis in all fields of genomics, and will greatly enhance the capacity to map and identify causal genes for various phenotypes.”

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