ArticleScience China. Life sciences2022
High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan.
Article in Science China. Life sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- The Genome of the Rice Variety Mowanggu Provides Insight Into Resistance to Magnaporthe oryzae.Molecular plant pathology · 2026Article
- Evaluating Blast Resistance of Huang-Huai Geng/Japonica Varieties Using Intragenic Markers.Rice (New York, N.Y.) · 2026Article
- Structural Variations Contribute to Subspeciation and Yield Heterosis in Rice.Plant biotechnology journal · 2025Article
- Comprehensive Analysis ofGenes · 2025Article
- Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR.Plant communications · 2024Article
- A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.National science review · 2024Article
- Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics.BMC genomic data · 2024Article
- Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae.Science China. Life sciences · 2024Article
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- A comprehensive overview of cotton genomics, biotechnology and molecular biological studies.Science China. Life sciences · 2023Review
- Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1.Science China. Life sciences · 2023Article
- Photoperiod Genes Contribute to Daylength-Sensing and Breeding in Rice.Plants (Basel, Switzerland) · 2023Article
- A chromosome-level genome assembly of an early matured aromaticFrontiers in plant science · 2023Article
- Haplotype analysis and marker development of five salt-tolerant-related genes in rice (Frontiers in plant science · 2023Article
- The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding.Plant biotechnology journal · 2022Article
- Chromosome-Level Genome Assembly of a FragrantInternational journal of molecular sciences · 2022Article
- Meta-analysis of QTLs and candidate genes associated with seed germination in rice (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Article
- Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Frontiers in plant science · 2022Article
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Abstract
High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two "golden quality" rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the "golden quality" rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.
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