Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens
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{"title"=>"Pyrosequencing for Mini-Barcoding of fresh and old museum specimens", "type"=>"journal", "authors"=>[{"first_name"=>"Shadi", "last_name"=>"Shokralla", "scopus_author_id"=>"22986167500"}, {"first_name"=>"Xin", "last_name"=>"Zhou", "scopus_author_id"=>"55743291200"}, {"first_name"=>"Daniel H.", "last_name"=>"Janzen", "scopus_author_id"=>"7006857631"}, {"first_name"=>"Winnie", "last_name"=>"Hallwachs", "scopus_author_id"=>"7801679641"}, {"first_name"=>"Jean François", "last_name"=>"Landry", "scopus_author_id"=>"7102087289"}, {"first_name"=>"Luke M.", "last_name"=>"Jacobus", "scopus_author_id"=>"6603952911"}, {"first_name"=>"Mehrdad", "last_name"=>"Hajibabaei", "scopus_author_id"=>"12240029000"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"362224303", "sgr"=>"79960825698", "pmid"=>"21818256", "scopus"=>"2-s2.0-79960825698", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0021252", "issn"=>"19326203"}, "id"=>"92321ca2-5292-3c78-acd5-280ebf82dd60", "abstract"=>"<p>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 <italic>c</italic> 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.</p>", "link"=>"http://www.mendeley.com/research/pyrosequencing-minibarcoding-fresh-old-museum-specimens", "reader_count"=>102, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Researcher"=>34, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>13, "Other"=>7, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Researcher"=>34, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>13, "Other"=>7, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>1, "Environmental Science"=>7, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>74, "Medicine and Dentistry"=>3, "Arts and Humanities"=>2, "Computer Science"=>5, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>74}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>7}, "Arts and Humanities"=>{"Arts and Humanities"=>2}}, "reader_count_by_country"=>{"New Zealand"=>1, "Argentina"=>1, "Sweden"=>1, "United States"=>2, "Australia"=>1, "France"=>2, "Germany"=>1, "Spain"=>1}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/751090"], "description"=>"<p>The red markers indicate the position of generated pyrosequences in comparison to the reference library, with blue markers, from BOLD or Genbank. Collection dates are shown in parentheses.</p>", "links"=>[], "tags"=>["trees", "kimura-2-parameter", "distances", "cytochrome", "oxidase", "mini-barcodes", "lepidoptera"], "article_id"=>421454, "categories"=>["Genetics"], "users"=>["Shadi Shokralla", "Xin Zhou", "Daniel H. Janzen", "Winnie Hallwachs", "Jean-François Landry", "Luke M. Jacobus", "Mehrdad Hajibabaei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021252.g001", "stats"=>{"downloads"=>4, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_NJ_trees_based_on_Kimura_2_Parameter_K2P_distances_for_cytochrome_c_oxidase_I_COI_mini_barcodes_of_old_museum_Lepidoptera_specimens_/421454", "title"=>"Neighbor-joining (NJ) trees based on Kimura-2-Parameter (K2P) distances for cytochrome <i>c</i> oxidase I (COI) mini-barcodes of old museum Lepidoptera specimens.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-27 00:24:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/378388", "https://ndownloader.figshare.com/files/378504"], "description"=>"<div><p>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 <em>c</em> 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.</p> </div>", "links"=>[], "tags"=>["pyrosequencing", "mini-barcoding", "specimens"], "article_id"=>134788, "categories"=>["Genetics"], "users"=>["Shadi Shokralla", "Xin Zhou", "Daniel H. Janzen", "Winnie Hallwachs", "Jean-François Landry", "Luke M. Jacobus", "Mehrdad Hajibabaei"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021252.s001", "https://dx.doi.org/10.1371/journal.pone.0021252.s002"], "stats"=>{"downloads"=>13, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pyrosequencing_for_Mini_Barcoding_of_Fresh_and_Old_Museum_Specimens/134788", "title"=>"Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-27 01:19:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/751217"], "description"=>"<p>Schematic representation of pyrosequencing vs. Sanger sequencing workflows.</p>", "links"=>[], "tags"=>["pyrosequencing", "sanger", "sequencing"], "article_id"=>421585, "categories"=>["Genetics"], "users"=>["Shadi Shokralla", "Xin Zhou", "Daniel H. Janzen", "Winnie Hallwachs", "Jean-François Landry", "Luke M. Jacobus", "Mehrdad Hajibabaei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021252.g002", "stats"=>{"downloads"=>4, "page_views"=>77, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_pyrosequencing_vs_Sanger_sequencing_workflows_/421585", "title"=>"Schematic representation of pyrosequencing vs. Sanger sequencing workflows.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-27 00:26:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/751374"], "description"=>"<p>Comparisons of DNA Pyrosequencing and Sanger sequencing results of the COI mini-barcode region.</p>", "links"=>[], "tags"=>["dna", "pyrosequencing", "sanger", "sequencing", "coi", "mini-barcode"], "article_id"=>421738, "categories"=>["Genetics"], "users"=>["Shadi Shokralla", "Xin Zhou", "Daniel H. Janzen", "Winnie Hallwachs", "Jean-François Landry", "Luke M. Jacobus", "Mehrdad Hajibabaei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021252.t001", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_DNA_Pyrosequencing_and_Sanger_sequencing_results_of_the_COI_mini_barcode_region_/421738", "title"=>"Comparisons of DNA Pyrosequencing and Sanger sequencing results of the COI mini-barcode region.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-27 00:28:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/751334"], "description"=>"<p>Primers used for PCR amplification and pyrosequencing.</p>", "links"=>[], "tags"=>["pcr", "amplification"], "article_id"=>421703, "categories"=>["Genetics"], "users"=>["Shadi Shokralla", "Xin Zhou", "Daniel H. Janzen", "Winnie Hallwachs", "Jean-François Landry", "Luke M. Jacobus", "Mehrdad Hajibabaei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021252.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_PCR_amplification_and_pyrosequencing_/421703", "title"=>"Primers used for PCR amplification and pyrosequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-27 00:28:23"}

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Relative Metric

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