ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
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- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 2022Article
- Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice.The Plant journal : for cell and molecular biology · 2020Article
- Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses inInternational journal of molecular sciences · 2020Article
- Characterization of the CommonGenes · 2020Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
- Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Frontiers in genetics · 2020Article
- TASUKE+: a web-based platform for exploring genome-wide association studies results and large-scale resequencing data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- The evolution study onJournal of genetics · 2019Article
- CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice.Plant physiology · 2019Article
- Development of introgression lines of AA genomeBreeding science · 2019Article
- Rice Galaxy: an open resource for plant science.GigaScience · 2019Article
- Assessing genome assembly quality using the LTR Assembly Index (LAI).Nucleic acids research · 2018Article
- Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.Nature genetics · 2018Article
- Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of RiceFrontiers in plant science · 2018Article
- Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide.Scientific reports · 2017Article
- Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.G3 (Bethesda, Md.) · 2017Article
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17 authors.
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Abstract
Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.
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