De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)

doi:10.1371/journal.pone.0097487

	De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)
	Peng Xianjun ; Teng Linhong 1; Wang Xiaoman 1; Wang Yucheng 1; Shen Shihua
	2014
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	9 期号:5
摘要	The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry.
学科领域	Multidisciplinary Sciences
DOI	10.1371/journal.pone.0097487
收录类别	SCI
语种	英语
WOS关键词	LIGNIN BIOSYNTHESIS ; PAPYRIFERA ; ANTIOXIDANT ; RESPONSES ; GROWTH
WOS研究方向	Science & Technology - Other Topics
WOS记录号	WOS:000336730600031
出版者	PUBLIC LIBRARY SCIENCE
文献子类	Article
出版地	SAN FRANCISCO
资助机构	foundation of the knowledge innovation project in the Chinese academy [KZCX2-YW-359-2] ; National Natural Science Foundation of China [31270653]
作者邮箱	shshen@ibcas.ac.cn
作品OA属性	gold, Green Published, Green Submitted
引用统计	被引频次：20[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27367
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Key Lab Plant Resources, Inst Bot, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Peng Xianjun,Teng Linhong,Wang Xiaoman,et al. De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)[J]. PLOS ONE,2014,9(5).
APA	Peng Xianjun,Teng Linhong,Wang Xiaoman,Wang Yucheng,&Shen Shihua.(2014).De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera).PLOS ONE,9(5).
MLA	Peng Xianjun,et al."De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)".PLOS ONE 9.5(2014).

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
Peng-2014-De Novo As（2472KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览请求全文