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

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...

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Autores principales: Serra, Lorrayne, Macchietto, Marissa, Macias-Muñoz, Aide, McGill, Cassandra Joan, Rodriguez, Isaryhia Maya, Rodriguez, Bryan, Murad, Rabi, Mortazavi, Ali
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686942/
https://www.ncbi.nlm.nih.gov/pubmed/31113823
http://dx.doi.org/10.1534/g3.119.400180
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author Serra, Lorrayne
Macchietto, Marissa
Macias-Muñoz, Aide
McGill, Cassandra Joan
Rodriguez, Isaryhia Maya
Rodriguez, Bryan
Murad, Rabi
Mortazavi, Ali
author_facet Serra, Lorrayne
Macchietto, Marissa
Macias-Muñoz, Aide
McGill, Cassandra Joan
Rodriguez, Isaryhia Maya
Rodriguez, Bryan
Murad, Rabi
Mortazavi, Ali
author_sort Serra, Lorrayne
collection PubMed
description 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.
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spelling pubmed-66869422019-08-11 Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome Serra, Lorrayne Macchietto, Marissa Macias-Muñoz, Aide McGill, Cassandra Joan Rodriguez, Isaryhia Maya Rodriguez, Bryan Murad, Rabi Mortazavi, Ali G3 (Bethesda) Genetics of Sex 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. Genetics Society of America 2019-05-21 /pmc/articles/PMC6686942/ /pubmed/31113823 http://dx.doi.org/10.1534/g3.119.400180 Text en Copyright © 2019 Serra et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genetics of Sex
Serra, Lorrayne
Macchietto, Marissa
Macias-Muñoz, Aide
McGill, Cassandra Joan
Rodriguez, Isaryhia Maya
Rodriguez, Bryan
Murad, Rabi
Mortazavi, Ali
Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title_full Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title_fullStr Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title_full_unstemmed Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title_short Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
title_sort hybrid assembly of the genome of the entomopathogenic nematode steinernema carpocapsae identifies the x-chromosome
topic Genetics of Sex
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686942/
https://www.ncbi.nlm.nih.gov/pubmed/31113823
http://dx.doi.org/10.1534/g3.119.400180
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