ArticleGenome biology2020
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed.
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- DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
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- Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.Molecular ecology · 2025Article
- The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.BMC biology · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- Comprehensive Analysis ofGenes · 2025Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Identification of a novel hybrid sterility locus S67 between temperate japonica subgroup and basmati subgroup in Oryza sativa L.Scientific reports · 2024Article
- TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.Genome biology · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- A chromosome-level genome of mango exclusively from long-read sequence data.The plant genome · 2024Article
- Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms.Breeding science · 2024Article
- Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus.Plant communications · 2024Article
- A syntelog-based pan-genome provides insights into rice domestication and de-domestication.Genome biology · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
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9 authors.
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Abstract
backgroundThe circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group's evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties.
resultsWe generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica-the rice group most closely related to circum-basmati-as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan.
conclusionThe availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.
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