IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.

Genomics, Proteomics & Bioinformatics
Jian SangZhang Zhang

Abstract

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implem...Continue Reading

Citations

Nov 12, 2020·Nucleic Acids Research·UNKNOWN CNCB-NGDC Members and Partners
Apr 15, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jacob I MarshDavid Edwards
May 27, 2021·Plant Biotechnology Journal·Zhengfeng ZhangGuoliang Li

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

HK
SAMtools
PASA
Coding Potential Calculator ( CPC )
GMAP
MEGA
BLASTX
BLAT
Cuffcompare
IC4R

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