NDLI: Genome re-sequencing and bioinformatics analysis of a nutraceutical rice

Content Provider	Springer Nature Link
Author	Lin, Juncheng Cheng, Zuxin Xu, Ming Huang, Zhiwei Yang, Zhijian Huang, Xinying Zheng, Jingui Lin, Tongxiang
Copyright Year	2014
Abstract	The genomes of two rice cultivars, Nipponbare and 93-11, have been well studied. However, there is little available genetic information about nutraceutical rice cultivars. To remedy this situation, the present study aimed to provide a basic genetic landscape of nutraceutical rice. The genome of Black-1, a black pericarp rice containing higher levels of anthocyanins, flavonoids, and a more potent antioxidant capacity, was sequenced at ≥30 × coverage using Solexa sequencing technology. The complete sequences of Black-1 genome shared more consensus sequences with indica cultivar 93-11 than with Nipponbare. With reference to the 93-11 genome, Black-1 contained 675,207 single-nucleotide polymorphisms, 43,130 insertions and deletions (1–5 bp), 1,770 copy number variations, and 10,911 presence/absence variations. These variations were observed to reside preferentially in Myb domains, NB-ARC domains and kinase domains, providing clues to the diversity of biological functions or secondary metabolisms in this cultivar. Intriguingly, 496 unique genes were identified by comparing it with the genomes of these two rice varieties; among the genes, 119 genes participate in the biosynthesis of secondary metabolites. Furthermore, several unique genes were predicted to be involved in the anthocyanins synthesis pathway. The genome-wide landscape of Black-1 uncovered by this study represents a valuable resource for further studies and for breeding nutraceutical rice varieties.
Starting Page	955
Ending Page	967
Page Count	13
File Format	PDF
ISSN	16174615
Journal	Molecular and General Genetics MGG
Volume Number	290
Issue Number	3
e-ISSN	16174623
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2014-12-10
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Black pericarp rice Single-nucleotide polymorphism INDEL Copy number variation Presence/absence variation Nutraceutical 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

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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
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