NDLI: Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening

Content Provider	Springer Nature Link
Author	Wang, Jia Dang, Zhenhua Zhang, Huirong Zheng, Linlin Borjigin, Tebuqin Wang, Yingchun
Copyright Year	2015
Abstract	Nitraria tangutorum Bobr., a valuable wild shrub distributed in Northwest China, produces edible and medicinal berries. However, little is known about the molecular mechanisms of its fruit development and ripening. We performed de novo transcriptome sequencing of N. tangutorum fruit using the Illumina HiSeq™ 2000 sequencing platform. More than 62.94 million reads were obtained and assembled into 69,306 unigenes (average length, 587 bp). These unigenes were annotated by querying against five databases (Nr, Swiss-Prot, GO, COG, and KEGG); 42,929 and 26,809 unigenes were found in the Nr and Swiss-Prot databases, respectively. In ortholog analyses, 33,363 unigenes were assigned with one or more GO terms, 15,537 hits were aligned to 25 COG classes, and 24,592 unigenes were classified into 128 KEGG pathways. Digital gene expression analyses were conducted on N. tangutorum fruit at the green (S1), yellow (S2), and red (S3) developmental stages. In total, 8240, 5985, and 4994 differentially expressed genes (DEGs) were detected for S1 vs. S2, S1 vs. S3, and S2 vs. S3, respectively. Cluster analyses showed that a large proportion of DEGs related to plant hormones and transcription factors (TFs) showed high expression in S1, down-regulated expression in S2, and up-regulated expression in S3. We analyzed the expression patterns of 23 genes encoding 12 putative enzymes involved in flavonoid biosynthesis. The expression profiles of 10 DEGs involved in flavonoid biosynthesis were validated by Q-PCR analysis. The assembled and annotated transcriptome sequences and gene expression profile analyses provide valuable genetic resources for research on N. tangutorum.
Starting Page	383
Ending Page	398
Page Count	16
File Format	PDF
ISSN	16174615
Journal	Molecular and General Genetics MGG
Volume Number	291
Issue Number	1
e-ISSN	16174623
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2015-09-20
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Nitraria tangutorum RNA-seq Digital gene expression profiling Fruit development and ripening Cell Biology Biochemistry Microbial Genetics and Genomics Plant Genetics & Genomics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Molecular Biology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Transcriptome profiling of non-climacteric ‘yellow’ melon during ripening: insights on sugar metabolism

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato

Dynamics of the chili pepper transcriptome during fruit development

RNA-seq-based transcriptome profiling reveals differential gene expression in the lungs of Sprague–Dawley rats during early-phase acute hypobaric hypoxia

A co-expression gene network associated with developmental regulation of apple fruit acidity

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

DNA array profiling of gene expression changes during maize embryo development

Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening

Similar Documents

Transcriptome profiling of non-climacteric ‘yellow’ melon during ripening: insights on sugar metabolism

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato

Dynamics of the chili pepper transcriptome during fruit development

RNA-seq-based transcriptome profiling reveals differential gene expression in the lungs of Sprague–Dawley rats during early-phase acute hypobaric hypoxia

A co-expression gene network associated with developmental regulation of apple fruit acidity

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

DNA array profiling of gene expression changes during maize embryo development

Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening