<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>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 <italic>de novo</italic> assembly of <italic>Steinernema feltiae</italic>, 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 <italic>de novo</italic> 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.</p>
</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.

A draft genome of a field-collected <italic>Steinernema feltiae</italic> strain NW

Journal of Nematology

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

A draft genome of a field-collected  strain NW

running-head

Advances in sequencing technologies have accelerated our understanding of the complex genetic network of organisms and genomic divergences that are linked to...

	Strain NW	Strain SN
Assembly
Total bases (bp)	121,603,260	82,627,153
No. of scaffolds	na	5,839
Scaffold N50	na	47,851
No. of contigs	4,678	59,024
Contig N50	60,433	3,650
No. of gaps (bp)	0	2,769,616
Longest scaffolds (bp)	1,315,981	1,446,875
No. of predicted genes	32,304	36,434
Total no. of amino acids	12,632,601	12,195,137
BUSCO assessment
Complete BUSCOs	87.27%	84.32%
Complete single copy	76.68%	80.55%
Complete duplicated copy	10.59%	3.77%
Fragmented	7.33%	8.15%
Missing	5.40%	7.54%
Alignment
Aligned Seqs	4,279 (91.47%)	5,418 (92.79%)
Aligned Bases	92,999,444 (76.48%)	74,444,081 (90.10%)
1-to-1	49,949	49,949
Total length (1-to-1)	72,468,269	72,538,432
Avg. identity (1-to-1)	97.07	97.07
M-to-M	133,667	133,667
Total length (M-to-M)	106,859,791	106,997,101
Avg. identity (M-to-M)	95.69	95.69
Genomic variation
Breakpoints	261,902	252,282
Relocations	8,456	5,231
Translocations	13,595	16,494
Inversions	1,411	1,952
Insertions	105,325	74,670
Total SNPs	907,706	907,706

A draft genome of a field-collected Steinernema feltiae strain NW

Published Online: Mar 17, 2020

Page range: 1 - 7

Received: Jul 23, 2019

DOI: https://doi.org/10.21307/jofnem-2020-003

Keywords
Entomopathogenic nematode, Biological control, Genome,

© 2020 Zhen Fu et al., published by Sciendo.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Figure 1:

Summary of the genome assembly of strain NW in comparison to strain SN.

A draft genome of a field-collected Steinernema feltiae strain NW

Published Online: Mar 17, 2020

Page range: 1 - 7

Received: Jul 23, 2019

DOI: https://doi.org/10.21307/jofnem-2020-003

KeywordsEntomopathogenic nematode, Biological control, Genome,

© 2020 Zhen Fu et al., published by Sciendo.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Figure 1:

Summary of the genome assembly of strain NW in comparison to strain SN.

Keywords
Entomopathogenic nematode, Biological control, Genome,