Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake
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{"title"=>"Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake", "type"=>"journal", "authors"=>[{"first_name"=>"Todd A.", "last_name"=>"Castoe", "scopus_author_id"=>"6602980445"}, {"first_name"=>"Alexander W.", "last_name"=>"Poole", "scopus_author_id"=>"36060109200"}, {"first_name"=>"A. P.Jason", "last_name"=>"de Koning", "scopus_author_id"=>"7005690019"}, {"first_name"=>"Kenneth L.", "last_name"=>"Jones", "scopus_author_id"=>"34975077500"}, {"first_name"=>"Diana F.", "last_name"=>"Tomback", "scopus_author_id"=>"6602723662"}, {"first_name"=>"Sara J.", "last_name"=>"Oyler-McCance", "scopus_author_id"=>"6603116295"}, {"first_name"=>"Jennifer A.", "last_name"=>"Fike", "scopus_author_id"=>"9639826600"}, {"first_name"=>"Stacey L.", "last_name"=>"Lance", "scopus_author_id"=>"6603745826"}, {"first_name"=>"Jeffrey W.", "last_name"=>"Streicher", "scopus_author_id"=>"33668015900"}, {"first_name"=>"Eric N.", "last_name"=>"Smith", "scopus_author_id"=>"7408612492"}, {"first_name"=>"David D.", "last_name"=>"Pollock", "scopus_author_id"=>"7202569082"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84856934143", "sgr"=>"84856934143", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0030953", "pmid"=>"22348032", "isbn"=>"1932-6203", "pui"=>"364261153"}, "id"=>"3e418fce-0b5c-3fbe-80ef-cfd5f09b8624", "abstract"=>"Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct ?Seq-to-SSR? approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample ? a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.", "link"=>"http://www.mendeley.com/research/rapid-microsatellite-identification-illumina-pairedend-genomic-sequencing-two-birds-snake", "reader_count"=>212, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>9, "Researcher"=>51, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>64, "Student > Postgraduate"=>11, "Student > Master"=>28, "Other"=>3, "Student > Bachelor"=>16, "Lecturer"=>3, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>9, "Researcher"=>51, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>64, "Student > Postgraduate"=>11, "Student > Master"=>28, "Other"=>3, "Student > Bachelor"=>16, "Lecturer"=>3, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>178, "Arts and Humanities"=>1, "Social Sciences"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>178}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>13}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>12, "Philippines"=>1, "Sudan"=>1, "United Kingdom"=>1, "Thailand"=>1, "Portugal"=>2, "New Zealand"=>1, "Canada"=>1, "Austria"=>1, "Sweden"=>1, "Finland"=>1, "Brazil"=>5, "Guatemala"=>1, "Italy"=>2, "Chile"=>2, "Nigeria"=>1, "Australia"=>1, "Germany"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/682926"], "description"=>"<p>Microsatellite loci were selected from the 5 million read datasets for each species that fit specific criteria for repeat monomer length (4–6), number of repeats observed (>7), and primer copy number in the observed data (variations shown above).</p>", "links"=>[], "tags"=>["stringent", "microsatellite"], "article_id"=>353406, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Highly_stringent_selection_of_choice_microsatellite_targets_/353406", "title"=>"Highly stringent selection of choice microsatellite targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-14 00:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/682814"], "description"=>"<p>The number of times a primer sequence or primer pair was observed in all data (from five million reads per species) was counted per species to approximate their genomic frequencies. Here the “Min (Fwd, Rev)” represents the minimum copy number of the forward and reverse primers observed in the data. The product of the independent frequencies of the forward and reverse primer sequences (per locus) is also shown (“Fwd×Rev Primer”), as is the frequency that each primer pair was observed together in a set of paired reads (“Primer Pair”).</p>", "links"=>[], "tags"=>["numbers", "flanking", "primer", "sequences", "amplifiable", "microsatellite", "loci"], "article_id"=>353283, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.g004", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Empirically_estimated_copy_numbers_of_identified_flanking_primer_sequences_for_potentially_amplifiable_microsatellite_loci_PALS_for_each_species_/353283", "title"=>"Empirically estimated copy numbers of identified flanking primer sequences for potentially amplifiable microsatellite loci (PALS) for each species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-14 00:54:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/682564"], "description"=>"<p>Analysis based on using five million Illumina long (114–116 bp) paired-end reads from a shotgun genomic library for each species.</p>", "links"=>[], "tags"=>["microsatellite", "loci", "amplifiable", "python"], "article_id"=>353044, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.g002", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_identification_of_microsatellite_loci_and_8216_potentially_amplifiable_microsatellite_loci_8217_PAL_among_bird_and_python_samples_/353044", "title"=>"Comparison of identification of microsatellite loci and ‘potentially amplifiable microsatellite loci’ (PAL) among bird and python samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-14 00:50:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/683072"], "description"=>"<p>Summary of microsatellite identification from various python and bird genome sequence sets.</p>", "links"=>[], "tags"=>["microsatellite", "python", "genome"], "article_id"=>353551, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_microsatellite_identification_from_various_python_and_bird_genome_sequence_sets_/353551", "title"=>"Summary of microsatellite identification from various python and bird genome sequence sets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-14 00:59:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/682474"], "description"=>"<p>Comparison based on the same number of reads for each platform (118,973 reads) sampled from Burmese python shotgun genomic libraries.</p>", "links"=>[], "tags"=>["microsatellite", "loci", "amplifiable", "illumina", "paired-end", "reads", "454"], "article_id"=>352942, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.g001", "stats"=>{"downloads"=>3, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_identification_of_microsatellite_loci_and_8216_potentially_amplifiable_microsatellite_loci_8217_PAL_using_Illumina_long_114_bp_paired_end_reads_versus_454_reads_/352942", "title"=>"Comparison of identification of microsatellite loci and ‘potentially amplifiable microsatellite loci’ (PAL) using Illumina long (114 bp) paired-end reads versus 454 reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-14 00:49:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/682685"], "description"=>"<p><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030953#s3\" target=\"_blank\">Results</a> based on five million Illumina long (114–116 bp) paired-end reads per species.</p>", "links"=>[], "tags"=>["microsatellite", "loci", "amplifiable", "4mer", "motifs", "birds"], "article_id"=>353157, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.g003", "stats"=>{"downloads"=>5, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_microsatellite_loci_and_8216_potentially_amplifiable_microsatellite_loci_8217_PAL_identification_for_4mer_repeat_motifs_in_birds_and_the_python_/353157", "title"=>"Comparison of microsatellite loci and ‘potentially amplifiable microsatellite loci’ (PAL) identification for 4mer repeat motifs in birds and the python.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-14 00:52:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/348826", "https://ndownloader.figshare.com/files/348900", "https://ndownloader.figshare.com/files/348956", "https://ndownloader.figshare.com/files/348996", "https://ndownloader.figshare.com/files/349014"], "description"=>"<div><p>Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require <em>a priori</em> selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, <em>Python molurus bivittatus</em>), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, <em>Centrocercus minimus</em>, and Clark's Nutcracker, <em>Nucifraga columbiana</em>), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.</p> </div>", "links"=>[], "tags"=>["microsatellite", "illumina", "paired-end", "genomic", "sequencing", "birds"], "article_id"=>128965, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0030953.s001", "https://dx.doi.org/10.1371/journal.pone.0030953.s002", "https://dx.doi.org/10.1371/journal.pone.0030953.s003", "https://dx.doi.org/10.1371/journal.pone.0030953.s004", "https://dx.doi.org/10.1371/journal.pone.0030953.s005"], "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rapid_Microsatellite_Identification_from_Illumina_Paired_End_Genomic_Sequencing_in_Two_Birds_and_a_Snake/128965", "title"=>"Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-14 02:29:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/683020"], "description"=>"<p>Comparison of microsatellite and PAL identification from Illumia paired-end reads versus 454 reads for the Burmese Python, broken down by microsatellite repeat motif length.</p>", "links"=>[], "tags"=>["microsatellite", "pal", "illumia", "paired-end", "reads", "454", "burmese", "motif"], "article_id"=>353490, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Todd A. Castoe", "Alexander W. Poole", "A. P. Jason de Koning", "Kenneth L. Jones", "Diana F. Tomback", "Sara J. Oyler-McCance", "Jennifer A. Fike", "Stacey L. Lance", "Jeffrey W. Streicher", "Eric N. Smith", "David D. Pollock"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030953.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_microsatellite_and_PAL_identification_from_Illumia_paired_end_reads_versus_454_reads_for_the_Burmese_Python_broken_down_by_microsatellite_repeat_motif_length_/353490", "title"=>"Comparison of microsatellite and PAL identification from Illumia paired-end reads versus 454 reads for the Burmese Python, broken down by microsatellite repeat motif length.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-14 00:58:10"}

PMC Usage Stats | Further Information

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Relative Metric

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