Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols
<p dir="ltr">Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However,...
محفوظ في:
| المؤلف الرئيسي: | |
|---|---|
| مؤلفون آخرون: | , , , , |
| منشور في: |
2021
|
| الموضوعات: | |
| الوسوم: |
إضافة وسم
لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!
|
| _version_ | 1864513553644388352 |
|---|---|
| author | Sonia Boughattas (508422) |
| author2 | Dana Albatesh (11721380) Albandari Al‐Khater (20402237) Bruno W. Giraldes (20402240) Asma A. Althani (17993884) Fatiha M. Benslimane (6695087) |
| author2_role | author author author author author |
| author_facet | Sonia Boughattas (508422) Dana Albatesh (11721380) Albandari Al‐Khater (20402237) Bruno W. Giraldes (20402240) Asma A. Althani (17993884) Fatiha M. Benslimane (6695087) |
| author_role | author |
| dc.creator.none.fl_str_mv | Sonia Boughattas (508422) Dana Albatesh (11721380) Albandari Al‐Khater (20402237) Bruno W. Giraldes (20402240) Asma A. Althani (17993884) Fatiha M. Benslimane (6695087) |
| dc.date.none.fl_str_mv | 2021-12-07T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1002/ece3.8447 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Whole_genome_sequencing_of_marine_organisms_by_Oxford_Nanopore_Technologies_Assessment_and_optimization_of_HMW_DNA_extraction_protocols/27991598 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Environmental sciences Environmental biotechnology DNA extraction marine species ONT sequencing protocol optimization whole genome sequencing |
| dc.title.none.fl_str_mv | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co‐precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples.</p><h2>Other Information</h2><p dir="ltr">Published in: Ecology and Evolution<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1002/ece3.8447" target="_blank">https://dx.doi.org/10.1002/ece3.8447</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_aa953114b8d9b5a9b8a7cdd8aa9b5b0e |
| identifier_str_mv | 10.1002/ece3.8447 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/27991598 |
| publishDate | 2021 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocolsSonia Boughattas (508422)Dana Albatesh (11721380)Albandari Al‐Khater (20402237)Bruno W. Giraldes (20402240)Asma A. Althani (17993884)Fatiha M. Benslimane (6695087)Biological sciencesGeneticsEnvironmental sciencesEnvironmental biotechnologyDNA extractionmarine speciesONT sequencingprotocol optimizationwhole genome sequencing<p dir="ltr">Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co‐precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples.</p><h2>Other Information</h2><p dir="ltr">Published in: Ecology and Evolution<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1002/ece3.8447" target="_blank">https://dx.doi.org/10.1002/ece3.8447</a></p>2021-12-07T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1002/ece3.8447https://figshare.com/articles/journal_contribution/Whole_genome_sequencing_of_marine_organisms_by_Oxford_Nanopore_Technologies_Assessment_and_optimization_of_HMW_DNA_extraction_protocols/27991598CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/279915982021-12-07T03:00:00Z |
| spellingShingle | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols Sonia Boughattas (508422) Biological sciences Genetics Environmental sciences Environmental biotechnology DNA extraction marine species ONT sequencing protocol optimization whole genome sequencing |
| status_str | publishedVersion |
| title | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| title_full | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| title_fullStr | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| title_full_unstemmed | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| title_short | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| title_sort | Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW‐DNA extraction protocols |
| topic | Biological sciences Genetics Environmental sciences Environmental biotechnology DNA extraction marine species ONT sequencing protocol optimization whole genome sequencing |