Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome

Background: Sinorhizobium fredii HH103 is a fast-growing rhizobial strain capable of infecting a broad range of legumes, including plants forming determinate and indeterminate nodules, such as Glycine max (its natural host) and Glycyrrhiza uralensis, respectively. Previous studies reported the seque...

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Autores: Fuentes Romero, Francisco, López Baena, Francisco Javier, Vinardell González, José María, Acosta Jurado, Sebastián
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Recursos:Universidad de Sevilla (US)
Repositorio:idUS. Depósito de Investigación de la Universidad de Sevilla
OAI Identifier:oai:idus.us.es:11441/177872
Acesso em linha:https://hdl.handle.net/11441/177872
https://doi.org/10.3390/genes16091094
Access Level:acceso abierto
Palavra-chave:Sinorhizobium fredii
Strain HH103
Sinorhizobium
Genome sequencing
PacBio
Illumina
Symbiotic plasmid
Transposable elements
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spelling Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 GenomeFuentes Romero, FranciscoLópez Baena, Francisco JavierVinardell González, José MaríaAcosta Jurado, SebastiánSinorhizobium frediiStrain HH103SinorhizobiumGenome sequencingPacBioIlluminaSymbiotic plasmidTransposable elementsBackground: Sinorhizobium fredii HH103 is a fast-growing rhizobial strain capable of infecting a broad range of legumes, including plants forming determinate and indeterminate nodules, such as Glycine max (its natural host) and Glycyrrhiza uralensis, respectively. Previous studies reported the sequence and annotation of the genome of this strain (7.25 Mb), showing the most complex S. fredii genome sequenced to date. It comprises seven replicons: one chromosome and six plasmids. Among these plasmids, pSfHH103d, also known as the symbiotic plasmid pSymA, harbors most of the genes involved in symbiosis. Due to limitations of the sequencing technology used at the time and the presence of high number of clusters of transposable elements, this plasmid could only be partially assembled as four separated contigs. Methods: In this work, we have used a combination of PacBio and Illumina sequencing technologies to resolve these complex regions, obtaining an updated genome sequence (7.27 Mb). Results: This updated version includes an increase in size of the largest replicons (chromosome, pSfHH103d, and pSfHH103e) and a complete and closed symbiotic plasmid (pSfHH103d or pSymA). Additionally, we carried out a re-annotation of the updated genome, merging the previous annotation and the new one found in the remaining gaps. Notably, we found a high number of transposable elements in the HH103 genome, especially in three plasmids (pSfHH103b, pSfHH103c, and pSymA), a feature that is common among S. fredii strains. Conclusions: The combination of PacBio and Illumina sequencing technologies has allowed us to obtain a complete version of the HH103 pSymA. The presence of a high number of mobile elements seems to be a general characteristic among S. fredii strains, a fact that might be related to a high genome plasticity.Multidisciplinary Digital Publishing Institute (MDPI)MicrobiologíaUniversidad de SevillaMinisterio de Ciencia e Innovación (MICIN). España2025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttps://hdl.handle.net/11441/177872https://doi.org/10.3390/genes16091094reponame:idUS. Depósito de Investigación de la Universidad de Sevillainstname:Universidad de Sevilla (US)InglésGenes, 16 (9), 1094.US1250546PID2022-141156OB-I00https://doi.org/10.3390/genes16091094info:eu-repo/semantics/openAccessoai:idus.us.es:11441/1778722026-06-17T12:51:07Z
dc.title.none.fl_str_mv Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
title Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
spellingShingle Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
Fuentes Romero, Francisco
Sinorhizobium fredii
Strain HH103
Sinorhizobium
Genome sequencing
PacBio
Illumina
Symbiotic plasmid
Transposable elements
title_short Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
title_full Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
title_fullStr Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
title_full_unstemmed Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
title_sort Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome
dc.creator.none.fl_str_mv Fuentes Romero, Francisco
López Baena, Francisco Javier
Vinardell González, José María
Acosta Jurado, Sebastián
author Fuentes Romero, Francisco
author_facet Fuentes Romero, Francisco
López Baena, Francisco Javier
Vinardell González, José María
Acosta Jurado, Sebastián
author_role author
author2 López Baena, Francisco Javier
Vinardell González, José María
Acosta Jurado, Sebastián
author2_role author
author
author
dc.contributor.none.fl_str_mv Microbiología
Universidad de Sevilla
Ministerio de Ciencia e Innovación (MICIN). España
dc.subject.none.fl_str_mv Sinorhizobium fredii
Strain HH103
Sinorhizobium
Genome sequencing
PacBio
Illumina
Symbiotic plasmid
Transposable elements
topic Sinorhizobium fredii
Strain HH103
Sinorhizobium
Genome sequencing
PacBio
Illumina
Symbiotic plasmid
Transposable elements
description Background: Sinorhizobium fredii HH103 is a fast-growing rhizobial strain capable of infecting a broad range of legumes, including plants forming determinate and indeterminate nodules, such as Glycine max (its natural host) and Glycyrrhiza uralensis, respectively. Previous studies reported the sequence and annotation of the genome of this strain (7.25 Mb), showing the most complex S. fredii genome sequenced to date. It comprises seven replicons: one chromosome and six plasmids. Among these plasmids, pSfHH103d, also known as the symbiotic plasmid pSymA, harbors most of the genes involved in symbiosis. Due to limitations of the sequencing technology used at the time and the presence of high number of clusters of transposable elements, this plasmid could only be partially assembled as four separated contigs. Methods: In this work, we have used a combination of PacBio and Illumina sequencing technologies to resolve these complex regions, obtaining an updated genome sequence (7.27 Mb). Results: This updated version includes an increase in size of the largest replicons (chromosome, pSfHH103d, and pSfHH103e) and a complete and closed symbiotic plasmid (pSfHH103d or pSymA). Additionally, we carried out a re-annotation of the updated genome, merging the previous annotation and the new one found in the remaining gaps. Notably, we found a high number of transposable elements in the HH103 genome, especially in three plasmids (pSfHH103b, pSfHH103c, and pSymA), a feature that is common among S. fredii strains. Conclusions: The combination of PacBio and Illumina sequencing technologies has allowed us to obtain a complete version of the HH103 pSymA. The presence of a high number of mobile elements seems to be a general characteristic among S. fredii strains, a fact that might be related to a high genome plasticity.
publishDate 2025
dc.date.none.fl_str_mv 2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/11441/177872
https://doi.org/10.3390/genes16091094
url https://hdl.handle.net/11441/177872
https://doi.org/10.3390/genes16091094
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genes, 16 (9), 1094.
US1250546
PID2022-141156OB-I00
https://doi.org/10.3390/genes16091094
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
dc.source.none.fl_str_mv reponame:idUS. Depósito de Investigación de la Universidad de Sevilla
instname:Universidad de Sevilla (US)
instname_str Universidad de Sevilla (US)
reponame_str idUS. Depósito de Investigación de la Universidad de Sevilla
collection idUS. Depósito de Investigación de la Universidad de Sevilla
repository.name.fl_str_mv
repository.mail.fl_str_mv
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