The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing
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{"title"=>"The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Chih Ming", "last_name"=>"Hung", "scopus_author_id"=>"55604636900"}, {"first_name"=>"Rong Chien", "last_name"=>"Lin", "scopus_author_id"=>"15757332800"}, {"first_name"=>"Jui Hua", "last_name"=>"Chu", "scopus_author_id"=>"55198043500"}, {"first_name"=>"Chia Fen", "last_name"=>"Yeh", "scopus_author_id"=>"35811487900"}, {"first_name"=>"Chiou Ju", "last_name"=>"Yao", "scopus_author_id"=>"55420952700"}, {"first_name"=>"Shou Hsien", "last_name"=>"Li", "scopus_author_id"=>"7409237107"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84874267094", "pmid"=>"23437111", "doi"=>"10.1371/journal.pone.0056301", "pui"=>"368400304", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "scopus"=>"2-s2.0-84874267094"}, "id"=>"acf14008-4333-31a3-b330-7f43d8be932e", "abstract"=>"The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.", "link"=>"http://www.mendeley.com/research/novo-assembly-mitochondrial-genomes-extinct-passenger-pigeon-ectopistes-migratorius-next-generation", "reader_count"=>52, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Uruguay"=>1, "Japan"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1004927"], "description"=>"<p>Read indicates the total numbers of 90 bp reads, % Q20 indicates the percentages of reads passing Q20 (the probability of a base call error ≤0.01), duplicate indicates the number of duplicate reads removed and assembled contig indicates the number of assembled contigs ≥300 bp.</p>", "links"=>[], "tags"=>["paired-end", "reads", "illumina", "genomic", "sequencing"], "article_id"=>665545, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_information_for_paired_end_reads_by_illumina_genomic_sequencing_of_two_passenger_pigeons_/665545", "title"=>"Sequence information for paired-end reads by illumina genomic sequencing of two passenger pigeons.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:32:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/1004907"], "description"=>"<p>We divided the mitogenome into regions encoding 22 transfer RNA genes (Phenylalanine [tRNA-Phe], Valine [tRNA-Val], Leucine [tRNA-Leu], Isoleucine [tRNA-Ile], Glutamine [tRNA-Gln], Methionine [tRNA-Met], Tryptophan [tRNA-Trp], Alanine [tRNA-Ala], Asparagine [tRNA-Asn], Cysteine [tRNA-Cys], Tyrosine [tRNA-Tyr], Serine [tRNA-Ser], Asparate [tRNA-Asp], Lysine [tRNA-Lys], Glycine [tRNA-Gly], Arginine [tRNA-Arg], Histidine [tRNA-His], Serine [tRNA-Ser], Leucine [tRNA-Leu], Threonine [tRNA-Thr], Proline [tRNA-Pro], Glutamate [tRNA-Glu]), 13 protein-coding genes (<i>NADH dehydrogenase subunit 1</i> [ND1], <i>NADH dehydrogenase subunit 2</i> [ND2], <i>cytochrome c oxidase subunit I</i> [COX1], <i>cytochrome c oxidase subunit II</i> [COX2], <i>ATP synthase F0 subunit 8</i> [ATP8], <i>ATP synthase F0 subunit 6</i> [ATP6], <i>cytochrome c oxidase subunit III</i> [COX3], <i>NADH dehydrogenase subunit 3</i> [ND3], <i>NADH dehydrogenase subunit 4L</i> [ND4L], <i>NADH dehydrogenase subunit 4</i> [ND4], <i>NADH dehydrogenase subunit 5</i> [ND5], <i>cytochrome b</i> [CYTB], <i>NADH dehydrogenase subunit 6</i> [ND6]), two ribosomal RNA genes (12 s rRNA and16 s rRNA) and a control region. Alignment length (bp), and number of segregating sites/number of nonsynonymous substitutions/number of gaps/number of ambiguous sites are shown for each of these regions. Numbers that are exceptionally high were bolded.</p>", "links"=>[], "tags"=>["divergence", "pigeon"], "article_id"=>665530, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.t002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_divergence_among_the_three_passenger_pigeon_mitogenomes_/665530", "title"=>"Pairwise divergence among the three passenger pigeon mitogenomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:32:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/957951", "https://ndownloader.figshare.com/files/957957"], "description"=>"<div><p>The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (<i>Ectopistes migratorius</i>) using <i>de novo</i> assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the <i>de novo</i> assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.</p> </div>", "links"=>[], "tags"=>["mitochondrial", "genomes", "extinct", "pigeon", "sequencing"], "article_id"=>628008, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0056301.s001", "https://dx.doi.org/10.1371/journal.pone.0056301.s002"], "stats"=>{"downloads"=>2, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_De_Novo_Assembly_of_Mitochondrial_Genomes_of_the_Extinct_Passenger_Pigeon_Ectopistes_migratorius_with_Next_Generation_Sequencing__/628008", "title"=>"The <em>De Novo</em> Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (<em>Ectopistes migratorius</em>) with Next Generation Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-21 18:08:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/957940"], "description"=>"<p>Percentage of non-duplicate reads blasted to chicken, human bacterial and fungal genome references downloaded from the NCBI genome database.</p>", "links"=>[], "tags"=>["illumina", "reads", "pads", "bmnh1149"], "article_id"=>627997, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.g003", "stats"=>{"downloads"=>1, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metagenomic_composition_of_the_Illumina_sequence_reads_from_the_toe_pads_of_two_passenger_pigeons_BMNH1149_and_BMNH1389_/627997", "title"=>"Metagenomic composition of the Illumina sequence reads from the toe pads of two passenger pigeons, BMNH1149 and BMNH1389.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 18:04:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/957935"], "description"=>"<p>Both mitogenomes start from the first base of tRNA-Phe.</p>", "links"=>[], "tags"=>["allele", "mitogenomes", "bmnh1149", "bmnh1389"], "article_id"=>627993, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.g002", "stats"=>{"downloads"=>0, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_coverage_in_red_and_frequency_of_the_major_allele_in_green_of_each_base_pair_along_the_mitogenomes_of_BMNH1149_upper_and_BMNH1389_lower_/627993", "title"=>"Sequence coverage (in red) and frequency of the major allele (in green) of each base pair along the mitogenomes of BMNH1149 (upper) and BMNH1389 (lower).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 18:02:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/957931"], "description"=>"<p>Arrows indicate the contigs that were annotated as the mitogenomes of passenger pigeons.</p>", "links"=>[], "tags"=>["contigs", "lengths", "assemblies", "illumina", "paired-end", "reads", "bmnh1149"], "article_id"=>627991, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.g001", "stats"=>{"downloads"=>1, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_sequence_coverage_of_contigs_against_their_lengths_bp_for_the_de_novo_assemblies_based_on_Illumina_paired_end_reads_of_A_BMNH1149_and_B_BMNH1389_/627991", "title"=>"Average sequence coverage of contigs against their lengths (bp) for the <i>de novo</i> assemblies based on Illumina paired-end reads of (A) BMNH1149 and (B) BMNH1389.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 18:01:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/957942"], "description"=>"<p>Frequency for 12 categories of sequence mismatches for raw read sequences against the consensus sequence of mitogenomes of BMNH1149 (in green) and BMNH1389 (in red).</p>", "links"=>[], "tags"=>["12", "categories", "mismatches", "sequences", "mitogenomes", "bmnh1149", "bmnh1389"], "article_id"=>627999, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Chih-Ming Hung", "Rong-Chien Lin", "Jui-Hua Chu", "Chia-Fen Yeh", "Chiou-Ju Yao", "Shou-Hsien Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0056301.g004", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_for_12_categories_of_sequence_mismatches_for_raw_read_sequences_against_the_consensus_sequence_of_mitogenomes_of_BMNH1149_in_green_and_BMNH1389_in_red_/627999", "title"=>"Frequency for 12 categories of sequence mismatches for raw read sequences against the consensus sequence of mitogenomes of BMNH1149 (in green) and BMNH1389 (in red).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 18:05:48"}

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Relative Metric

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