cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11402079
title: Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes

description: ABSTRACT 

Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, as well as a short duplication at the target site. It has been noted that, when observing extant IS element copies in a genome, occasionally no Target Site Duplication (TSD) is readily identifiable. This has been attributed to degeneration of the TSD at some point after the insertion event. Here, we provide evidence that some IS movement events – namely, those that occur in association with large-scale genome rearrangements – occur without generating TSDs. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5/IS1182 movement plus a large deletion in Escherichia coli C. Additionally, we use sequencing data from the Lenski long-term evolution experiment to provide a further 14 examples of IS150 movements in E. coli B that are associated with large deletions and do not carry TSDs. Overall, our results indicate that some IS elements can insert into, and thus repair, existing DNA breaks in bacterial genomes.

 

REPOSITORY CONTENTS

This entry contains additional raw data and background information for the manuscript entitled: Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes 

01_SBW25_Dup_IS: contains the background files for work on the SBW25-Dup-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces- stability test R code and output

02_Ec_Del_IS: contains the background files for work on the Ec-Del-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces

03_LTEE: contains the background files for work on 3x LTEE populations (at 60,000 generations), including:- raw sequencing reads (downloaded from NCBI BioProject database; accession number PRJNA380528)- breseq output for Ara-3, Ara-6, and Ara+1 populations- reference alignment file (NCBI RefSeq NC_012967.1)
DOI: 10.5281/zenodo.11402078
title: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes

description: ABSTRACT

Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, and a short duplication at the target site. It has been noted that for some extant IS element copies there are no Target Site Duplication (TSD) readily identifiable. The absence of TSDs has been attributed to degeneration of the TSD at some point after the insertion event, recombination between identical insertion sequences, or adjacent deletions. Indeed, the latter two - recombination between IS copies and adjacent deletions - are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long term evolution experiment. Furthermore, we propose that some IS movement events – namely, those that occur in association with large-scale genome rearrangements – do not generate TSDs, and occur without evidence for recombination between IS copies or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5 movement plus a large deletion in Escherichia coli C. Although unlikely, it is possible that the observed deletion and associated IS movement may have occurred in two successive events in a single overnight culture a novel insertion followed by an adjacent deletion. However, the presence of an IS at the center of a large-scale duplication is not readily explained, and suggests that IS element activity may not only cause large-scale deletions, but may also affect the likelihood of duplications. 

 

REPOSITORY CONTENTS

This entry contains additional raw data and background information for the manuscript entitled: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes 

01_SBW25_Dup_IS: contains the background files for work on the SBW25-Dup-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces- stability test R code and output

02_Ec_Del_IS: contains the background files for work on the Ec-Del-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces

03_LTEE: contains the background files for work on 3x LTEE populations (at 60,000 generations), including:- raw sequencing reads (downloaded from NCBI BioProject database; accession number PRJNA380528)- breseq output for Ara-3, Ara-6, and Ara+1 populations- reference alignment file (NCBI RefSeq NC_012967.1)
DOI: 10.5281/zenodo.13888852
title: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes

description: ABSTRACT

Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, and a short duplication at the target site. It has been noted that for some extant IS element copies there are no Target Site Duplication (TSD) readily identifiable. The absence of TSDs has been attributed to degeneration of the TSD at some point after the insertion event, recombination between identical insertion sequences, or adjacent deletions. Indeed, the latter two - recombination between IS copies and adjacent deletions - are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long term evolution experiment. Furthermore, we propose that some IS movement events – namely, those that occur in association with large-scale genome rearrangements – do not generate TSDs, and occur without evidence for recombination between IS copies or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5 movement plus a large deletion in Escherichia coli C. Although unlikely, it is possible that the observed deletion and associated IS movement may have occurred in two successive events in a single overnight culture a novel insertion followed by an adjacent deletion. However, the presence of an IS at the center of a large-scale duplication is not readily explained, and suggests that IS element activity may not only cause large-scale deletions, but may also affect the likelihood of duplications. 

 

REPOSITORY CONTENTS

This entry contains additional raw data and background information for the manuscript entitled: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes 

01_SBW25_Dup_IS: contains the background files for work on the SBW25-Dup-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces- stability test R code and output

02_Ec_Del_IS: contains the background files for work on the Ec-Del-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces

03_LTEE: contains the background files for work on 3x LTEE populations (at 60,000 generations), including:- raw sequencing reads (downloaded from NCBI BioProject database; accession number PRJNA380528)- breseq output for Ara-3, Ara-6, and Ara+1 populations- reference alignment file (NCBI RefSeq NC_012967.1)
DOI: 10.15468/dl.bkttyf
title: Occurrence Download

description: A dataset containing 540 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hemimycena gracilis (Quél.) Singer"
 ]
}

 The dataset includes 540 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040501-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sg8amd
title: Occurrence Download

description: A dataset containing 74304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Micrastur semitorquatus (Vieillot, 1817)"
 ]
}

 The dataset includes 74304 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040500-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25901/njz4-we39
title: Red Dirt Melon Farm Flux Data Release 2024_v2
DOI: 10.15468/dl.hawbnz
title: Occurrence Download

description: A dataset containing 21301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphorbia heterophylla L."
 ]
}

 The dataset includes 21301 records from 520 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040502-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25901/b6kx-0w83
title: Ridgefield Flux Data Release 2024_v2
DOI: 10.15468/dl.fu35xt
title: Occurrence Download

description: A dataset containing 3939 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucoagaricus americanus (Peck) Vellinga"
 ]
}

 The dataset includes 3939 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040504-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c24aav
title: Occurrence Download

description: A dataset containing 5998 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "IucnRedListCategory is one of (CR, EN, VU)",
 "TaxonKey is Aves",
 "Year 2020-2020"
 ]
}

 The dataset includes 5998 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040503-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qk9ax8
title: Occurrence Download

description: A dataset containing 16145540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Solanales, Brassicales)"
 ]
}

 The dataset includes 16145540 records from 7634 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040480-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rrvvhu
title: Occurrence Download

description: A dataset containing 1235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Zonotrichia leucophrys nuttalli Ridgway, 1899",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month May-August"
 ]
}

 The dataset includes 1235 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057302-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-70515
title: Gold Cup race at Hollywood park, 1958

description: 17 images. Gold Cup race at Hollywood park, 12 July 1958. Ralph Lowe (owner of "Gallant Man"); Mr and Mrs. John Nerud; Mr. and Mrs. Mervyn Leroy; Linda Leroy; Eddie Schmidt; Colonel and Mrs. L.G. Burns; Nancy Heinz Russell; Walker Mullen; Babs Lipstreu. (General views of races); (Shot of mother swan and babies).; Caption slip reads: "Photographer: Jensen. Date: 1958-07-12. Assignment: Holly Park. Flash 5 minutes. 92/93: Babs Lipstreu (Wheeling, West Va making pix [sic] of race. Action Dev. 8 minutes. 78: 1st race finish and crowd. 79: 2nd race start, num. 10 winner reves up for adorable. 48: 3rd race after start. 49: 3rd race photo finish number 5, 1st; number 7, 2nd".; Caption slip reads: "Photographer: Miller. Date: 07-12. Reporter: Spencer. Assignment: Gold Cup -- taken director's room. 5/6: Eddie Schmidt, Mrs. L.G. Burns, Col. L.G. Burns. Burnses own horse Eddie Schmidt after man on left was named. 47/48: Ralph Lowe, owner of Gallant Man. Mr. and Mrs. John A. Nerud (he, trainer). Taken in director's room. 215/16: Nancy Heinz Russell, Walker Mullen. 11/12: Linda Leroy, Mr. and Mrs. Mervyn Leroy; he's pres. of Holly P".; Caption slip reads: "Photographer: Monte. Date: 1958-07-12. Assignment: Holly Park, action. 35: Back streatch [sic] of 1st race. 36: Shot of mama and papa swans with babies (1 mo. old). 9/10: Crowd shots start and finish 2nd race. 51: Clubhouse turn 3rd race".
DOI: 10.15468/dl.ehdcbj
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidopterys cavaleriei H.Lév."
 ]
}

 The dataset includes 43 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019775-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f8sdtb
title: Occurrence Download

description: A dataset containing 4651701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2019-2020"
 ]
}

 The dataset includes 4651701 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037635-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhuej8
title: Occurrence Download

description: A dataset containing 645 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.37663 -4.55555,-69.02786 -4.55555,-68.96353 0.00344,-75.92987 0.16883,-74.37663 -4.55555))",
 "HasGeospatialIssue is false",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 645 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060617-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-67730
title: Society -- Food feature, 1958

description: 8 images. Society -- Food feature, 6 June 1958. Chef Joseph Faussone; Mrs. Harold Field; Mrs. Leslie Lindell; Doctor Everett Lambertson; Mrs. Raphael G. Dunleux; Doctor R.G. Donlevy. (Sleeve reads: S-12367).; Caption slip reads: "Photographer: Wilson. Date: 1958-06-05. Reporter: 'Soc.'. Assignment: Food -- Ambassador. 00/01: Hors D'ourves). 13/14: Kitchen shot -- Chef Joseph Faussone; Mrs. Harold Field. 98/99: L/R -- Mrs. Leslie Lindell; Dr. Everett R. Lambertson; Mrs. Raphael G. Dunleux; & Dr. R.G. Dunlevy. 27/28: Close up of Crown of Lamb (main dish) individual serving".
DOI: 10.15468/dl.gbnmhf
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ephedra rupestris Benth.",
 "Country is Peru",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057303-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cd3w72
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus brevidens Freyn & Sint."
 ]
}

 The dataset includes 38 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019761-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-68196
title: Mens wearing apparel show at Biltmore, 1958

description: 2 images. Mens wearing apparel show at Biltmore, 22 June 1958. Wanda Harding; Harry Zigmond (both models); Lee Schertzer (model); Michael Schertzer -- 9 years (model).; Caption slip reads: "Photographer: Lapp. Date: 1958-06-22. Reporter: Ostler. Assignment: Mens Wearing apparel show Biltmore Hotel. 29/30: Look-alikes in car coats displayed by Wanda Harding of San Diego and Harry Zigmond, Hollywood. 15/16: Sweater shot... Lee Schertzer models newest in men sweater wear-- long sleeve striped cardigan, with bell sleeves and shawl collor of striped Thalspun fabric. Boy is his son, Michael, 9".
DOI: 10.15468/dl.h9mrdr
title: Occurrence Download

description: A dataset containing 1114576 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.71928 51.38855,-3.86721 51.42387,-3.68903 51.44259,-3.59009 52.14005,-4.81278 52.13764,-5.50946 51.954,-5.35306 51.61097,-4.75591 51.51374,-4.3304 51.47249,-3.82878 51.36636,-3.76454 51.37991,-3.71928 51.38855))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 1114576 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001528-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wznay
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Escallonia resinosa (Ruiz & Pav.) Pers.",
 "Country is Peru",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 85 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057305-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8r26jc
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Philautus abditus Inger, Orlov & Darevsky, 1999"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019798-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-27143
title: City Council, 1951

description: 4 images. City Council, 29 November 1951. Ransom M. Callicott, President, California Restaurant Association; Henry Rio, Deputy City Clerk; John Holland, Councilman; George P. Cron, Councilman; Don A. Allen, Councilman; Philip Draus, Counsel for Local Office, Office for Price Stabilization.
DOI: 10.15468/dl.8g5xwu
title: Occurrence Download

description: A dataset containing 909778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "TaxonKey is Corylus avellana L."
 ]
}

 The dataset includes 909778 records from 2668 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001527-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7a8kgj
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camissoniopsis confusa (P.H.Raven) W.L.Wagner & Hoch"
 ]
}

 The dataset includes 354 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116916-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ne93p6
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-120.14648 12.77163,-92.25 12.25,-104.15039 30.48892,-119.75 33.75,-120.14648 12.77163))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cynoscion parvipinnis Ayres, 1861"
 ]
}

 The dataset includes 268 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0307272-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxnskg
title: Occurrence Download

description: A dataset containing 3864292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3864292 records from 698 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048479-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2sqw82
title: Occurrence Download

description: A dataset containing 424 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camonea bifida (Vahl) Raf."
 ]
}

 The dataset includes 424 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116939-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nalavn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is observe_tuna_bycatch_ecoscope"
 ]
}

 The dataset includes 0 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010667-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykvddw
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Espadarana durrellorum (Cisneros-Heredia, 2007)"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0307290-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.