Genome skimming herbarium specimens for DNA barcoding and phylogenomics
Abstract Background The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges...
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| Format: | Article |
| Language: | English |
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BMC
2018-06-01
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| Series: | Plant Methods |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13007-018-0300-0 |
| _version_ | 1828875869178822656 |
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| author | Chun-Xia Zeng Peter M. Hollingsworth Jing Yang Zheng-Shan He Zhi-Rong Zhang De-Zhu Li Jun-Bo Yang |
| author_facet | Chun-Xia Zeng Peter M. Hollingsworth Jing Yang Zheng-Shan He Zhi-Rong Zhang De-Zhu Li Jun-Bo Yang |
| author_sort | Chun-Xia Zeng |
| collection | DOAJ |
| description | Abstract Background The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today’s next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Results As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA. Conclusions The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction. |
| first_indexed | 2024-12-13T08:09:44Z |
| format | Article |
| id | doaj.art-16d36b85787a456eb5d5284ea86bd5d4 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-13T08:09:44Z |
| publishDate | 2018-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-16d36b85787a456eb5d5284ea86bd5d42022-12-21T23:54:15ZengBMCPlant Methods1746-48112018-06-0114111410.1186/s13007-018-0300-0Genome skimming herbarium specimens for DNA barcoding and phylogenomicsChun-Xia Zeng0Peter M. Hollingsworth1Jing Yang2Zheng-Shan He3Zhi-Rong Zhang4De-Zhu Li5Jun-Bo Yang6Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesRoyal Botanic Garden EdinburghGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesAbstract Background The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today’s next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Results As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA. Conclusions The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.http://link.springer.com/article/10.1186/s13007-018-0300-0Degraded DNAHerbarium specimensGenome skimmingPlastid genomerDNADNA barcoding |
| spellingShingle | Chun-Xia Zeng Peter M. Hollingsworth Jing Yang Zheng-Shan He Zhi-Rong Zhang De-Zhu Li Jun-Bo Yang Genome skimming herbarium specimens for DNA barcoding and phylogenomics Plant Methods Degraded DNA Herbarium specimens Genome skimming Plastid genome rDNA DNA barcoding |
| title | Genome skimming herbarium specimens for DNA barcoding and phylogenomics |
| title_full | Genome skimming herbarium specimens for DNA barcoding and phylogenomics |
| title_fullStr | Genome skimming herbarium specimens for DNA barcoding and phylogenomics |
| title_full_unstemmed | Genome skimming herbarium specimens for DNA barcoding and phylogenomics |
| title_short | Genome skimming herbarium specimens for DNA barcoding and phylogenomics |
| title_sort | genome skimming herbarium specimens for dna barcoding and phylogenomics |
| topic | Degraded DNA Herbarium specimens Genome skimming Plastid genome rDNA DNA barcoding |
| url | http://link.springer.com/article/10.1186/s13007-018-0300-0 |
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