NDLI: Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

Content Provider	PubMed Central
Author	Shadi, Shokralla Zhou, Xin Janzen, Daniel H. Hallwachs, Winnie Landry, Jean-françois Jacobus, Luke M. Hajibabaei, Mehrdad
Editor	Kolokotronis, Sergios-orestis
Copyright Year	2011
Abstract	DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53–97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.
Related Links	http://dx.doi.org/10.1371/journal.pone.0021252
Starting Page	21252
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	7
Volume Number	6
Language	English
Publisher	Public Library of Science
Publisher Date	2011-07-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

DNA Extraction from Museum Specimens of Parasitic Hymenoptera

Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

A Novel Mini-DNA Barcoding Assay to Identify Processed Fins from Internationally Protected Shark Species

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

Implications of Pyrosequencing Error Correction for Biological Data Interpretation

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

Similar Documents

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

DNA Extraction from Museum Specimens of Parasitic Hymenoptera

Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

A Novel Mini-DNA Barcoding Assay to Identify Processed Fins from Internationally Protected Shark Species

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

Implications of Pyrosequencing Error Correction for Biological Data Interpretation

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens