Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa
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{"title"=>"Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid alfalfa", "type"=>"journal", "authors"=>[{"first_name"=>"Zhipeng", "last_name"=>"Liu", "scopus_author_id"=>"55606268700"}, {"first_name"=>"Tianlong", "last_name"=>"Chen", "scopus_author_id"=>"56006317100"}, {"first_name"=>"Ma", "last_name"=>"Lichao", "scopus_author_id"=>"57199676053"}, {"first_name"=>"Zhiguang", "last_name"=>"Zhao", "scopus_author_id"=>"22837396800"}, {"first_name"=>"Patrick X.", "last_name"=>"Zhao", "scopus_author_id"=>"35265529600"}, {"first_name"=>"Zhibiao", "last_name"=>"Nan", "scopus_author_id"=>"55606321600"}, {"first_name"=>"Yanrong", "last_name"=>"Wang", "scopus_author_id"=>"7601514335"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84892576614", "doi"=>"10.1371/journal.pone.0083549", "pui"=>"372134047", "issn"=>"19326203", "pmid"=>"24349529", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84892576614"}, "id"=>"07e555a1-9ec7-331d-9ff2-48e9e958dbda", "abstract"=>"BACKGROUND: Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. The large size and complexity of the alfalfa genome has delayed the development of genomic resources for alfalfa research. Second-generation Illumina transcriptome sequencing is an efficient method for generating a global transcriptome sequence dataset for gene discovery and molecular marker development in alfalfa.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: More than 28 million sequencing reads (5.64 Gb of clean nucleotides) were generated by Illumina paired-end sequencing from 15 different alfalfa tissue samples. In total, 40,433 unigenes with an average length of 803 bp were obtained by de novo assembly. Based on a sequence similarity search of known proteins, a total of 36,684 (90.73%) unigenes were annotated. In addition, 1,649 potential EST-SSRs were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 100 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 82 were able to amplify sequences in initial screening tests, and 27 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 10 alfalfa accessions.\\n\\nCONCLUSIONS/SIGNIFICANCE: The present study provided global sequence data for autotetraploid alfalfa and demonstrates the Illumina platform is a fast and effective approach to EST-SSR markers development in alfalfa. The use of these transcriptome datasets will serve as a valuable public information platform to accelerate studies of the alfalfa genome.", "link"=>"http://www.mendeley.com/research/global-transcriptome-sequencing-using-illumina-platform-development-estssr-markers-autotetraploid-al", "reader_count"=>22, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Master"=>8, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Master"=>8, "Other"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>2, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Belgium"=>1, "Brazil"=>1, "Portugal"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1312520"], "description"=>"<p>(A) Callus cells. (B) Germinated seeds (36 hours after seed germination). (C) Germinated seeds (48 hours after seed germination). (D) Roots from a 20-day-old seedling. (E) Cotyledons from a 7-day-old seedling. (F) Unifoliate leaves from a 20-day-old seedling. (G) Compound leaves. (H) Young stem (less lignified). (I) Middle stem (moderately lignified). (J) Old stem (more lignified). (K) Shoot apex. (L) Young inflorescence (diameter 0.4-0.5 cm). (M) Mature inflorescence (diameter 2 cm), (N) Young pod (16 days after pollination). (O) Mature pod (24 days after pollination).</p>", "links"=>[], "tags"=>["tissues", "samples", "alfalfa", "cultivar"], "article_id"=>875843, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_tissues_used_in_this_study_and_all_samples_shown_are_from_the_alfalfa_cultivar_8220_Golden_queen_8221_/875843", "title"=>"The tissues used in this study and all samples shown are from the alfalfa cultivar “Golden queen”.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312522"], "description"=>"<p>Plot showing the dependence of unigene length on the number of reads assembled into each unigene.</p>", "links"=>[], "tags"=>["dependence", "unigene", "reads", "assembled"], "article_id"=>875845, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plot_showing_the_dependence_of_unigene_length_on_the_number_of_reads_assembled_into_each_unigene_/875845", "title"=>"Plot showing the dependence of unigene length on the number of reads assembled into each unigene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312523"], "description"=>"<p>A BLAST search was performed with a cutoff E-value <10E-10 between <i>M. truncatula</i> and <i>M. sativa</i> on the basis of coding sequence similarity. </p>", "links"=>[], "tags"=>["unigene"], "article_id"=>875846, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g003", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_ratio_of_M_sativa_unigene_length_to_M_truncatula_unigene_coverage_depth_/875846", "title"=>"The ratio of <i>M. sativa</i> unigene length to <i>M. truncatula</i> unigene coverage depth.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312525"], "description"=>"<p>White lines represent alfalfa unigenes that were not mapped to the <i>M. truncatula</i> genome sequence assembly, and black lines represent alfalfa unigenes that were mapped to the <i>M. truncatula</i> genome.</p>", "links"=>[], "tags"=>["unigenes", "mapped", "pseudomolecules"], "article_id"=>875848, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alfalfa_unigenes_mapped_to_Mt3_5_2_pseudomolecules_with_a_threshold_of_95_identity_and_90_coverage_/875848", "title"=>"Alfalfa unigenes mapped to Mt3.5.2 pseudomolecules with a threshold of 95% identity and 90% coverage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312526"], "description"=>"<p>A total of 14,415 unigenes with BLAST matches to known proteins were assigned to three main categories: cellular component, molecular function and biological process.</p>", "links"=>[], "tags"=>["ontology", "classification", "assembled", "unigenes"], "article_id"=>875849, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_GO_classification_of_assembled_unigenes_in_M_sativa_/875849", "title"=>"Gene Ontology (GO) classification of assembled unigenes in <i>M. sativa</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312528"], "description"=>"<p>In total, 8,522 of the 40,433 sequences with Nr hits were grouped into 25 COG classifications.</p>", "links"=>[], "tags"=>["orthologous", "groups"], "article_id"=>875851, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clusters_of_orthologous_groups_COG_classification_/875851", "title"=>"Clusters of orthologous groups (COG) classification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312529"], "description"=>"<p>Each accession includes five individual plants. The corresponding detailed information from 10 alfalfa accessions is displayed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083549#pone.0083549.s001\" target=\"_blank\">Table S1</a>. The letter ‘M’ denotes the molecular markers, which are 300 bp, 200 bp, and 150 bp (top to bottom) in Ms-29, and 200 bp, 150 bp, and 100 bp in Ms-39.</p>", "links"=>[], "tags"=>["variations", "ms-29", "ms-39", "loci", "10", "alfalfa"], "article_id"=>875852, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083549.g007", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_EST_SSR_variations_at_the_Ms_29_and_Ms_39_loci_of_10_alfalfa_accessions_/875852", "title"=>"EST-SSR variations at the Ms-29 and Ms-39 loci of 10 alfalfa accessions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-12 02:57:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1312532", "https://ndownloader.figshare.com/files/1312533", "https://ndownloader.figshare.com/files/1312535", "https://ndownloader.figshare.com/files/1312536", "https://ndownloader.figshare.com/files/1312537", "https://ndownloader.figshare.com/files/1312538"], "description"=>"<div><p>Background</p><p>Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. The large size and complexity of the alfalfa genome has delayed the development of genomic resources for alfalfa research. Second-generation Illumina transcriptome sequencing is an efficient method for generating a global transcriptome sequence dataset for gene discovery and molecular marker development in alfalfa.</p> <p>Methodology/Principal Findings</p><p>More than 28 million sequencing reads (5.64 Gb of clean nucleotides) were generated by Illumina paired-end sequencing from 15 different alfalfa tissue samples. In total, 40,433 unigenes with an average length of 803 bp were obtained by <i>de</i><i>novo</i> assembly. Based on a sequence similarity search of known proteins, a total of 36,684 (90.73%) unigenes were annotated. In addition, 1,649 potential EST-SSRs were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 100 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 82 were able to amplify sequences in initial screening tests, and 27 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 10 alfalfa accessions.</p> <p>Conclusions/Significance</p><p>The present study provided global sequence data for autotetraploid alfalfa and demonstrates the Illumina platform is a fast and effective approach to EST-SSR markers development in alfalfa. The use of these transcriptome datasets will serve as a valuable public information platform to accelerate studies of the alfalfa genome.</p> </div>", "links"=>[], "tags"=>["transcriptome", "sequencing", "illumina", "est-ssr", "markers", "autotetraploid"], "article_id"=>875855, "categories"=>["Biological Sciences"], "users"=>["Zhipeng Liu", "Tianlong Chen", "Lichao Ma", "Zhiguang Zhao", "Patrick X. Zhao", "Zhibiao Nan", "Yanrong Wang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0083549.s001", "https://dx.doi.org/10.1371/journal.pone.0083549.s002", "https://dx.doi.org/10.1371/journal.pone.0083549.s003", "https://dx.doi.org/10.1371/journal.pone.0083549.s004", "https://dx.doi.org/10.1371/journal.pone.0083549.s005", "https://dx.doi.org/10.1371/journal.pone.0083549.s006"], "stats"=>{"downloads"=>23, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_Transcriptome_Sequencing_Using_the_Illumina_Platform_and_the_Development_of_EST_SSR_Markers_in_Autotetraploid_Alfalfa_/875855", "title"=>"Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-12 02:57:34"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Biotechnology", "average_usage"=>[259, 472, 622, 759, 885, 1009, 1123, 1232, 1335, 1437, 1533, 1627, 1698]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[269, 451, 577, 699, 812, 922, 1019, 1126, 1225, 1309, 1404, 1493, 1563]}]}
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