Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1783442646224601088 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6686942 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT serralorrayne hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT macchiettomarissa hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT maciasmunozaide hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT mcgillcassandrajoan hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT rodriguezisaryhiamaya hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT rodriguezbryan hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT muradrabi hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome AT mortazaviali hybridassemblyofthegenomeoftheentomopathogenicnematodesteinernemacarpocapsaeidentifiesthexchromosome |