Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum

doi:10.1007/s11103-013-0135-z

	Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum
	Zhang, Ting 1,2; Zhao, Xiuqin 1; Wang, Wensheng 1; Huang, Liyu 1; Liu, Xiaoyue 1; Zong, Ying 1; Zhu, Linghua 1; Yang, Daichang 2; Fu, Binying 1; Li, Zhikang 1
刊名	PLANT MOLECULAR BIOLOGY
	2014
卷号	84 期号:3 页码:315-327
关键词	Sorghum propinquum Transcriptome Illumina sequencing Aerial-shoot Rhizome
ISSN号	0167-4412
DOI	10.1007/s11103-013-0135-z
通讯作者	Zhang, Ting
英文摘要	Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOT-MOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.
学科主题	Biochemistry & Molecular Biology ; Plant Sciences
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000330980600006
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4934]
专题	作物科学研究所_分子生物学系
作者单位	1.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China 2.Wuhan Univ, Coll Life Sci, State Key Lab Hybrid Rice, Wuhan 430072, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Ting,Zhao, Xiuqin,Wang, Wensheng,et al. Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum[J]. PLANT MOLECULAR BIOLOGY,2014,84(3):315-327.
APA	Zhang, Ting.,Zhao, Xiuqin.,Wang, Wensheng.,Huang, Liyu.,Liu, Xiaoyue.,...&Li, Zhikang.(2014).Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum.PLANT MOLECULAR BIOLOGY,84(3),315-327.
MLA	Zhang, Ting,et al."Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum".PLANT MOLECULAR BIOLOGY 84.3(2014):315-327.