AI Article Synopsis
- In 2002, the first crop genome of the rice cultivar 93-11 was published, serving as a reference for super-hybrid rice, but it wasn't updated until now.
- The study utilized advanced sequencing techniques to create a more complete and accurate genome assembly for 93-11, enabling better analysis of its genetic features compared to the Nipponbare genome.
- The improved genome data revealed important gene expression patterns during seed development and variations that can aid in targeted breeding efforts for rice.
Article Abstract
In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of groups in molecular breeding programs.
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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8813773 | PMC |
| http://dx.doi.org/10.3389/fpls.2021.769700 | DOI Listing |
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