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. 2019 Aug 8;9(8):2687-2697.
doi: 10.1534/g3.119.400180.

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Lorrayne Serra  1 , Marissa Macchietto  2 , Aide Macias-Muñoz  1 , Cassandra Joan McGill  1 , Isaryhia Maya Rodriguez  1 , Bryan Rodriguez  1 , Rabi Murad  1 , Ali Mortazavi  3   4
Affiliations

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Lorrayne Serra et al. G3 (Bethesda). .

Abstract

Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.

Keywords: Genetics of Sex; S. carpocapsae; Steinernema; Steinernema genome.

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Figures

Figure 1
Figure 1
Identifying the X chromosome in S. carpocapsae. (A) Illumina sequencing of females (orange) and males (blue) shows coverage in order of longest to shortest for scaffolds >1 Mb, in which scaffold 0 is chromosome X. (B) Gene density calculated for 100 kb intervals. (C) GC content for every 100 kb with a sliding window of 1 kb. (D) Number of repeats per 100 kb.
Figure 2
Figure 2
Macrosynteny between S. carpocapsae and C. elegans. C. elegans one-to-one orthologous genes had their position predicted in the S. carpocapsae assembly. Each rectangle represents the fraction of C. elegans genes present per 500 kb window in S. carpocapsae. Red rectangle indicates no synteny.
Figure 3
Figure 3
Protease expansion in S. carpocapsae. A) Location of metalloprotease genes on S. carpocapsae scaffolds. Darker bands represent gene overlap or gene clusters. Red bands represent venom component-encoding genes. B) Location of serine proteases on S. carpocapsae scaffolds. Darker bands represent gene overlap or gene clusters. Red bands represent venom component-encoding genes. C) Maximum-likelihood phylogenetic tree of metalloproteases in S. carpocapsae and their orthologs in C. elegans (highlighted yellow) using a bootstrap support of 100 replicates. Gene names highlighted in red represent genes encoding metalloprotease venom components. D) Maximum-likelihood phylogenetic tree of genes encoding serine protease venom components in S. carpocapsae and their orthologs in C. elegans (highlighted yellow) using a bootstrap support of 100 replicates. Gene names highlighted in red represent venomous serine protease.
Figure 4
Figure 4
Gene expression profiling of S. carpocapsae development in 11 embryonic stages and 11 post-IJ development. (A) Heatmap showing 26,761 genes with minimum of 1 transcript per million (TPM). (B) Volcano plot of 12,461 differentially expressed genes with minimum of 1 TPM, between male (blue) and female (orange) and representative GO terms. (C) Principal Component Analysis of all genes expressed in embryos and during an activation time course. Developmental stages are separated from major life stages (IJ, adults) by PC3.
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