Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.

Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Xiaobai Li, Jie Luo, Tianlian Yan, Lin Xiang, Feng Jin, Dehui Qin, Chongbo Sun, Ming Xie
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dfc83872823048e19c00c34d23391673
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:dfc83872823048e19c00c34d23391673
record_format	dspace
spelling	oai:doaj.org-article:dfc83872823048e19c00c34d233916732021-11-18T08:39:13ZDeep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.1932-620310.1371/journal.pone.0085480https://doaj.org/article/dfc83872823048e19c00c34d233916732013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24392013/?tool=EBIhttps://doaj.org/toc/1932-6203Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.Xiaobai LiJie LuoTianlian YanLin XiangFeng JinDehui QinChongbo SunMing XiePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e85480 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xiaobai Li Jie Luo Tianlian Yan Lin Xiang Feng Jin Dehui Qin Chongbo Sun Ming Xie Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
description	Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.
format	article
author	Xiaobai Li Jie Luo Tianlian Yan Lin Xiang Feng Jin Dehui Qin Chongbo Sun Ming Xie
author_facet	Xiaobai Li Jie Luo Tianlian Yan Lin Xiang Feng Jin Dehui Qin Chongbo Sun Ming Xie
author_sort	Xiaobai Li
title	Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
title_short	Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
title_full	Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
title_fullStr	Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
title_full_unstemmed	Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
title_sort	deep sequencing-based analysis of the cymbidium ensifolium floral transcriptome.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/dfc83872823048e19c00c34d23391673
work_keys_str_mv	AT xiaobaili deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT jieluo deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT tianlianyan deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT linxiang deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT fengjin deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT dehuiqin deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT chongbosun deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome AT mingxie deepsequencingbasedanalysisofthecymbidiumensifoliumfloraltranscriptome
_version_	1718421532286386176

Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.

Ejemplares similares