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Abstract
Advances in sequencing technologies have accelerated our understanding of the complex genetic network of organisms and genomic divergences that are linked to evolutionary processes. While many model organisms and laboratory strains have been sequenced, wild populations are underrepresented in the growing list of sequenced genomes. Here, we present a de novo assembly of Steinernema feltiae, strain NW, collected from a working agricultural field in south central Washington, USA. Leveraging Pacific Biosciences (PacBio) long reads, we sequenced strain NW to a high depth (99×). The resulting de novo assembly is significantly larger than the previous assembly generated from the laboratory strain SN, with a noticeable improvement in continuity and completeness. Comparative analysis of two assemblies revealed numerous single nucleotide polymorphisms (SNPs), breakpoints, and indels present between the two genomes. This alternative genome resource and annotation could benefit the research community to examine the genetic foundation of evolutionary processes as well as genomic variation among conspecific populations.
Highlights
The genome encodes the entire inheritance messages of living organisms, serving as the foundation for biological, cellular, and molecular processes that are essential for development and reproduction
The entomopathogenic nematode Steinernema feltiae is widely applied to control insect pests, such as scarab larvae, fungus gnats, and lepidopteran larvae (Toba et al, 1983; Jess and Bingham, 2004; Lacey et al, 2006; Lacey and Georgis, 2012)
The work presented here improves the current genome resources for this species in a few ways, including improving the continuity and the completeness of the draft genome. This resource represents a draft genome of a naturally occurring strain that was collected from a working agricultural field, which could be phylogenetically divergent from its laboratory counterpart that was sequenced previously (Palková, 2004; Barriere and Felix, 2005)
Summary
The genome encodes the entire inheritance messages of living organisms, serving as the foundation for biological, cellular, and molecular processes that are essential for development and reproduction. The rapid progress of high-throughput sequencing and computational algorithms have begun to enable sequencing of field-collected species and strains (Wang et al, 2018; Wu et al, 2018; Kingan et al, 2019), which could be divergent from their laboratory-maintained congeners due to the lack of artificial selections (Palková, 2004; Barriere and Felix, 2005) Scrutinizing these wild populations and species might shed light on genetic changes during both domestication processes and natural selection, paving the way for better biodiversity conservation, trait selection, and targeted breeding (Fuentes-Pardo and Ruzzante, 2017; Wang et al, 2018; Wu et al, 2018). A genomic resource from a field-collected entomopathogenic strain could offer valuable insights into local adaptation as well as trait improvement for this broadly applied biopesticide
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