Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice

Autor: Zhi Zhang, Yang Yu, Jian-Ping Lian, Yu-Wei Yang, Yan-Zhao Feng, Huang He, Meng-Qi Lei, Yue-Qin Chen, Yu-Chan Zhang, Yan-Fei Zhou
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0106 biological sciences
0301 basic medicine
agronomic traits
cultivated rice
01 natural sciences
Japonica
Domestication
Exon
crop domestication
wild rice
Biology (General)
Spectroscopy
Conserved Sequence
Genetics
Plant evolution
conservation
food and beverages
General Medicine
Exons
Computer Science Applications
Chemistry
RNA
Plant
RNA
Long Noncoding
Crops
Agricultural
QH301-705.5
lncRNAs
Biology
Catalysis
Article
Inorganic Chemistry
03 medical and health sciences
Species Specificity
Sequence Homology
Nucleic Acid
microRNA
Physical and Theoretical Chemistry
Molecular Biology
Gene
QD1-999
Gene Library
Oryza sativa
Base Sequence
Organic Chemistry
fungi
RNA
Molecular Sequence Annotation
Oryza
biology.organism_classification
030104 developmental biology
Transcriptome
Sequence Alignment
010606 plant biology & botany
Genome-Wide Association Study
Zdroj: International Journal of Molecular Sciences, Vol 22, Iss 4742, p 4742 (2021)
International Journal of Molecular Sciences
Volume 22
Issue 9
ISSN: 1661-6596
1422-0067
Popis: Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
Databáze: OpenAIRE
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