Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics

Area of Science:

• Genomics
• Plant Science
• Agricultural Science

Background:

• The initial 93-11 rice genome assembly from 2002, crucial for indica cultivars, required an update.
• The existing assembly lacked completeness and was not suitable as a reference for indica sequencing data.

Purpose of the Study:

• To generate a gap-less, high-quality genome assembly for the rice cultivar 93-11.
• To provide a reliable reference genome for indica rice cultivars and facilitate molecular breeding.

Main Methods:

• Utilized ultra-depth single molecule real-time (SMRT) reads and Hi-C sequencing.
• Employed a reference-guided and gap-closing strategy to refine the genome assembly.

Main Results:

• Achieved a gap-less genome assembly for the 93-11 rice cultivar.
• Identified differences in genome collinearity and gene content compared to the Nipponbare reference.
• Transcriptome data revealed correlations between gene expression and seed development stages.

Conclusions:

• The updated 93-11 genome assembly is a superior reference for indica cultivar sequencing.
• Genomic variations, including alternative splicing in starch synthesis genes and waxy gene variations, offer potential for targeted breeding.
• This high-quality genome resource will advance the understanding of Oryza group genome structures and functions in breeding programs.