Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods e...
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| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2014/434575 |
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| _version_ | 1832554271796625408 |
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| author | Momchilo Vuyisich Ayesha Arefin Karen Davenport Shihai Feng Cheryl Gleasner Kim McMurry Beverly Parson-Quintana Jennifer Price Matthew Scholz Patrick Chain |
| author_facet | Momchilo Vuyisich Ayesha Arefin Karen Davenport Shihai Feng Cheryl Gleasner Kim McMurry Beverly Parson-Quintana Jennifer Price Matthew Scholz Patrick Chain |
| author_sort | Momchilo Vuyisich |
| collection | DOAJ |
| description | Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used. |
| format | Article |
| id | doaj-art-27011e63fe2c41258048ee7065fe3392 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-27011e63fe2c41258048ee7065fe33922025-02-03T05:51:56ZengWileyInternational Journal of Genomics2314-436X2314-43782014-01-01201410.1155/2014/434575434575Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNAMomchilo Vuyisich0Ayesha Arefin1Karen Davenport2Shihai Feng3Cheryl Gleasner4Kim McMurry5Beverly Parson-Quintana6Jennifer Price7Matthew Scholz8Patrick Chain9Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USAParkview Medical Center School for Medical Laboratory Science, 400 West 16th Street, Pueblo, CO 81003, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USALos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USASequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.http://dx.doi.org/10.1155/2014/434575 |
| spellingShingle | Momchilo Vuyisich Ayesha Arefin Karen Davenport Shihai Feng Cheryl Gleasner Kim McMurry Beverly Parson-Quintana Jennifer Price Matthew Scholz Patrick Chain Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA International Journal of Genomics |
| title | Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA |
| title_full | Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA |
| title_fullStr | Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA |
| title_full_unstemmed | Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA |
| title_short | Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA |
| title_sort | facile high quality sequencing of bacterial genomes from small amounts of dna |
| url | http://dx.doi.org/10.1155/2014/434575 |
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