Genome announcement ofSteinernema khuongiand its associated symbiont from Florida

Abstract

Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest are biological control agents, namely, native entomopathogenic nematodes (EPN) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. While the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other entomopathogenic nematodes and its symbionts to understand host range and habitat suitability.

Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematodeSteinernema hermaphroditum

“…2019; Baniya et al . 2019; Baniya and DiGennaro 2021). Because the skpo-2 locus is X-linked in both S. hermaphroditum and S. carpocapsae , it is hemizygous in males; it is likely also X-linked in all other Steinernema nematodes, whose X chromosomes have not yet been identified.…”

“…The skpo-2 locus is exceptionally well suited to serve as such as a marker: we could readily recover Shm-skpo-2 mutants on the basis of their easily recognized phenotype, and Shm-skpo-2 dumpy mutants are healthy and mate well as males. In each of the seven Steinernema species for which sequence is available, there is one skpo-2 gene (Dillman et al 2015;Serra et al 2019;Baniya et al 2019;Baniya and DiGennaro 2021). Because the skpo-2 locus is X-linked in both S. hermaphroditum and S. carpocapsae, it is hemizygous in males; it is likely also X-linked in all other Steinernema nematodes, whose X chromosomes have not yet been identified.…”

“…Homology searches of additional Steinernema nematodes were performed using BLAST 2.2.24+ on a Debian GNU server (Altschul et al 1990) (Dillman et al 2015;Serra et al 2019;Baniya et al 2019;Baniya and DiGennaro 2021). MEGA11 software (Tamura et al 2021) was used to generate a neighbor-joining phylogeny using peroxidase protein sequences from C. elegans version WS290 (Davis et al 2022) and from S. hermaphroditum GCA_030435675.1.…”

Nematode genome announcement: The draft genome sequence of entomopathogenic nematode Heterorhabditis indica

“…Genome completeness using Core Eukaryotic Genes Mapping Approach (CEGMA) (Parra et al, 2007) against 248 ultra-conserved core eukaryotic genes showed 97.17% completeness. A total of 10,494 protein-coding genes were predicted in the H. indica Hms1-i20 by SNAP (Korf, 2004), Augustus (Stanke and Morgenstern, 2005), GeneMark (Besemer and Borodovsky, 2005), and Maker (Cantarel et al, 2008). Functional annotation by NCBI Blastx+/ RefSeq/SwissProt/UniProt databases resulted in the annotation of 9,596 genes.…”

“…Genomic information about EPNs is scant in the public domain. Presently, whole-genome information is available for only one heterorhabditid and seven steinernematid nematodes ( Lu et al, 2016 ; Baniya and DiGennaro, 2021 ). Here, we present the first draft genome sequence assembly for Heterorhabditis indica , which is widely present in the warmer and tropical climatic regions and is one of the most commercialized EPNs ( Lacey and Georgis, 2012 ).…”