Crop Genomics Research

Improved Genome Sequence of Japonica Rice Cultivar Nipponbare Reveals Over 3,000 New Genes

Researchers have improved the haplotype-resolved genome sequence of the japonica rice cultivar Nipponbare, identifying over 3,000 new genes.

Key Takeaways:

  1. Researchers have improved the haplotype-resolved genome sequence of the japonica rice cultivar Nipponbare, identifying over 3,000 new genes.
  2. The enhanced genome assembly addresses gaps in the original sequence due to repetitive DNA, providing a more comprehensive reference.
  3. The study, published in Tropical Plants, utilized advanced sequencing techniques to generate a more complete telomere-to-telomere (T2T) genome.
  4. The refined genome assembly significantly advances rice genetic studies and breeding programs.
  5. The research highlights the importance of continuous technological advancements in accurately mapping complex plant genomes.

Improved Genome Sequence of Japonica Rice Cultivar Nipponbare Reveals Over 3,000 New Genes

A research team has reported an improvement in the haplotype-resolved genome sequence of the japonica rice cultivar Nipponbare. This enhancement has led to identifying and annotating more than 3,000 new genes, potentially contributing to advancements in crop improvement and breeding strategies.

Enhancing the Nipponbare Reference Genome

The japonica rice cultivar Nipponbare has been a key reference in rice genomics since its initial sequencing two decades ago. Despite advancements in sequencing technology, unresolved gaps in the Nipponbare genome assembly have persisted, primarily due to repetitive DNA sequences. Recent efforts have focused on improving genome assemblies in various rice species, including telomere sequencing, but achieving a fully haplotype-resolved assembly has remained a challenge.

Advanced Sequencing Techniques Yield Improvements

A study published in Tropical Plants on April 3, 2024, reported an improved haplotype-resolved rice genome, achieving a comprehensive telomere-to-telomere (T2T) assembly. The research utilized PacBio HiFi and Hi-C reads to generate a contig assembly with Hifiasm, resulting in a haplotype-phased assembly. This process produced distinct contigs for nine chromosomes, while the remaining three required two.

The assembled contigs were then organized into 12 pseudo-chromosomes using the YaHS scaffolding tool, resulting in a T2T assembly that was larger and more complete than the previous IRGSP-1.0 reference. This refined assembly revealed the presence of 3,050 new genes, with more than 95% supported by transcript evidence, enhancing the genome’s annotation and structural understanding.

Implications for Rice Genetics and Breeding Programs

The study’s findings suggest that new sequencing technologies have significant potential to expand and refine genomic data, improving the genetic information available for established genomes. The extended and more detailed genome, covering 99.3% of universal single-copy genes with an N50 of 30.7 Mb, provides a solid framework for further rice genetic studies and breeding programs. Comparative analysis also highlighted structural variants and additional non-aligning regions, adding to the understanding of genomic architecture and functionality.

“This phased genome will be a useful resource for rice research,” stated Robert J. Henry, the study’s lead researcher. The team plans to apply sequencing and assembly techniques to other rice varieties and closely related species.

Read the complete study here.

Photo by Sandy Ravaloniaina on Unsplash

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