De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl.
Publication Date
June 14, 2017
Authors
Congcong Liu, Ying Dou, Xuelian Guan, Qiang Fu, et al
Volume
12
Issue
6
Pages
e0179219
DOI
https://dx.plos.org/10.1371/journal.pone.0179219
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0179219
Scopus
85020720286
Mendeley
http://www.mendeley.com/research/novo-transcriptomic-analysis-development-estssrs-sorbus-pohuashanensis-hance-hedl
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Mendeley | Further Information

{"title"=>"De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl.", "type"=>"journal", "authors"=>[{"first_name"=>"Congcong", "last_name"=>"Liu", "scopus_author_id"=>"57194545518"}, {"first_name"=>"Ying", "last_name"=>"Dou", "scopus_author_id"=>"57194551153"}, {"first_name"=>"Xuelian", "last_name"=>"Guan", "scopus_author_id"=>"55753436900"}, {"first_name"=>"Qiang", "last_name"=>"Fu", "scopus_author_id"=>"57194540196"}, {"first_name"=>"Ze", "last_name"=>"Zhang", "scopus_author_id"=>"57194547925"}, {"first_name"=>"Zenghui", "last_name"=>"Hu", "scopus_author_id"=>"55541014300"}, {"first_name"=>"Jian", "last_name"=>"Zheng", "scopus_author_id"=>"56574538700"}, {"first_name"=>"Yizeng", "last_name"=>"Lu", "scopus_author_id"=>"57194540785"}, {"first_name"=>"Wei", "last_name"=>"Li", "scopus_author_id"=>"56795879800"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0179219", "sgr"=>"85020720286", "scopus"=>"2-s2.0-85020720286", "isbn"=>"1111111111", "pmid"=>"28614366", "pui"=>"616783187"}, "id"=>"180bd665-512f-36ed-aa4c-8b653d9fa9e3", "abstract"=>"© 2017 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database), 35,225 unigenes were annotated using the GO (Gene Ontology categories) database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups). Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR) site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.", "link"=>"http://www.mendeley.com/research/novo-transcriptomic-analysis-development-estssrs-sorbus-pohuashanensis-hance-hedl", "reader_count"=>5, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Master"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Master"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Agricultural and Biological Sciences"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Computer Science"=>{"Computer Science"=>1}}, "group_count"=>0}

Scopus | Further Information

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