De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Genetics and Molecular Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300480 |
Resumo: | Abstract Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes were identified as differentially expressed between flowers and leaves, and used in further enrichment analysis. Also, 2,156 unigenes were annotated as transcription factors. Furthermore, our transcriptome analysis resulted in the identification of candidate unigenes annotated to enzymes involved in terpenoid biosynthesis. Taken together, this work has laid the foundation for the investigation of secondary metabolite biosynthesis and other physiological processes of D. schraderiana. |
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Genetics and Molecular Biology |
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De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderianaDysphania schraderianade novo assemblytranscriptomeannotationterpenoid biosynthesisAbstract Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes were identified as differentially expressed between flowers and leaves, and used in further enrichment analysis. Also, 2,156 unigenes were annotated as transcription factors. Furthermore, our transcriptome analysis resulted in the identification of candidate unigenes annotated to enzymes involved in terpenoid biosynthesis. Taken together, this work has laid the foundation for the investigation of secondary metabolite biosynthesis and other physiological processes of D. schraderiana.Sociedade Brasileira de Genética2019-06-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300480Genetics and Molecular Biology v.42 n.2 2019reponame:Genetics and Molecular Biologyinstname:Sociedade Brasileira de Genética (SBG)instacron:SBG10.1590/1678-4685-gmb-2018-0033info:eu-repo/semantics/openAccessFu,SuhongLei,MingZhang,YongqunDeng,ZhaominShi,JingHao,Doudoueng2019-08-27T00:00:00Zoai:scielo:S1415-47572019000300480Revistahttp://www.gmb.org.br/ONGhttps://old.scielo.br/oai/scielo-oai.php||editor@gmb.org.br1678-46851415-4757opendoar:2019-08-27T00:00Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG)false |
dc.title.none.fl_str_mv |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
title |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
spellingShingle |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana Fu,Suhong Dysphania schraderiana de novo assembly transcriptome annotation terpenoid biosynthesis |
title_short |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
title_full |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
title_fullStr |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
title_full_unstemmed |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
title_sort |
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana |
author |
Fu,Suhong |
author_facet |
Fu,Suhong Lei,Ming Zhang,Yongqun Deng,Zhaomin Shi,Jing Hao,Doudou |
author_role |
author |
author2 |
Lei,Ming Zhang,Yongqun Deng,Zhaomin Shi,Jing Hao,Doudou |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Fu,Suhong Lei,Ming Zhang,Yongqun Deng,Zhaomin Shi,Jing Hao,Doudou |
dc.subject.por.fl_str_mv |
Dysphania schraderiana de novo assembly transcriptome annotation terpenoid biosynthesis |
topic |
Dysphania schraderiana de novo assembly transcriptome annotation terpenoid biosynthesis |
description |
Abstract Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes were identified as differentially expressed between flowers and leaves, and used in further enrichment analysis. Also, 2,156 unigenes were annotated as transcription factors. Furthermore, our transcriptome analysis resulted in the identification of candidate unigenes annotated to enzymes involved in terpenoid biosynthesis. Taken together, this work has laid the foundation for the investigation of secondary metabolite biosynthesis and other physiological processes of D. schraderiana. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-06-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300480 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300480 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/1678-4685-gmb-2018-0033 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
Genetics and Molecular Biology v.42 n.2 2019 reponame:Genetics and Molecular Biology instname:Sociedade Brasileira de Genética (SBG) instacron:SBG |
instname_str |
Sociedade Brasileira de Genética (SBG) |
instacron_str |
SBG |
institution |
SBG |
reponame_str |
Genetics and Molecular Biology |
collection |
Genetics and Molecular Biology |
repository.name.fl_str_mv |
Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG) |
repository.mail.fl_str_mv |
||editor@gmb.org.br |
_version_ |
1752122389336948736 |