De Novo Assembly and Annotation of Salvia splendens Transcriptome Using the Illumina Platform
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{"title"=>"De novo assembly and annotation of Salvia splendens transcriptome using the illumina platform", "type"=>"journal", "authors"=>[{"first_name"=>"Xiuxiu", "last_name"=>"Ge", "scopus_author_id"=>"56108493900"}, {"first_name"=>"Hongwei", "last_name"=>"Chen", "scopus_author_id"=>"56108889300"}, {"first_name"=>"Hongli", "last_name"=>"Wang", "scopus_author_id"=>"56108899100"}, {"first_name"=>"Aiping", "last_name"=>"Shi", "scopus_author_id"=>"56108384500"}, {"first_name"=>"Kefeng", "last_name"=>"Liu", "scopus_author_id"=>"55729544700"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84898004399", "doi"=>"10.1371/journal.pone.0087693", "scopus"=>"2-s2.0-84898004399", "pui"=>"372799703", "pmid"=>"24622329"}, "id"=>"54b2ef03-7800-3247-aa0e-4b431630eef9", "abstract"=>"BACKGROUND: As an important perennial herbaceous flower, Salvia splendens possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although Salvia splendens is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for Salvia splendens through de novo high-throughput transcriptome sequencing.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We performed de novo transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for Salvia splendens were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).\\n\\nCONCLUSIONS: We obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of Salvia splendens in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on Salvia splendens.", "link"=>"http://www.mendeley.com/research/novo-assembly-annotation-salvia-splendens-transcriptome-using-illumina-platform", "reader_count"=>23, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>5, "Student > Master"=>6, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>5, "Student > Master"=>6, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>19, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"Brazil"=>1, "Serbia and Montenegro"=>1, "Mexico"=>1, "Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/1417184", "https://ndownloader.figshare.com/files/1417185"], "description"=>"<div><p>Background</p><p>As an important perennial herbaceous flower, <i>Salvia splendens</i> possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although <i>Salvia splendens</i> is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for <i>Salvia splendens</i> through <i>de novo</i> high-throughput transcriptome sequencing.</p><p>Methodology/Principal Findings</p><p>We performed <i>de novo</i> transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for <i>Salvia splendens</i> were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).</p><p>Conclusions</p><p>We obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of <i>Salvia splendens</i> in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on <i>Salvia splendens</i>.</p></div>", "links"=>[], "tags"=>["Agricultural biotechnology", "bioethics", "Computational biology", "genomics", "Genome analysis tools", "transcriptomes", "Genome expression analysis", "Plant science", "Plant biotechnology", "Plant genomics", "plants", "Flowering plants", "flowers", "annotation", "transcriptome", "illumina"], "article_id"=>959679, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Xiuxiu Ge", "Hongwei Chen", "Hongli Wang", "Aiping Shi", "Kefeng Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087693.s001", "https://dx.doi.org/10.1371/journal.pone.0087693.s002"], "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_Novo_Assembly_and_Annotation_of_Salvia_splendens_Transcriptome_Using_the_Illumina_Platform/959679", "title"=>"<i>De Novo</i> Assembly and Annotation of <i>Salvia splendens</i> Transcriptome Using the Illumina Platform", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-12 03:33:28"}

PMC Usage Stats | Further Information

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Relative Metric

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