Back to Search
Start Over
Genome sequence of the model rice variety KitaakeX
- Source :
- BMC Genomics, 20, BMC Genomics, BMC Genomics, Vol 20, Iss 1, Pp 1-9 (2019), BMC genomics, vol 20, iss 1
- Publication Year :
- 2019
- Publisher :
- Research Square Platform LLC, 2019.
-
Abstract
- Background: The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results: Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions: The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.<br />BMC Genomics, 20<br />ISSN:1471-2164
- Subjects :
- 0106 biological sciences
Kitaake
Sequence assembly
Medical and Health Sciences
01 natural sciences
Genome
Whole genome sequence
2. Zero hunger
0303 health sciences
Contig
food and beverages
Genomics
Biological Sciences
Phenotype
1305 Biotechnology
590 Animals (Zoology)
Functional genomics
Genome, Plant
Research Article
Biotechnology
KitaakeX
lcsh:QH426-470
Bioinformatics
lcsh:Biotechnology
Computational biology
XA21 immune receptor
Biology
Oryza
DNA sequencing
10127 Institute of Evolutionary Biology and Environmental Studies
03 medical and health sciences
1311 Genetics
Information and Computing Sciences
lcsh:TP248.13-248.65
Genetics
Gene
030304 developmental biology
Whole genome sequencing
Oryza sativa
Whole Genome Sequencing
Zhenshan97
Nipponbare
fungi
Human Genome
Computational Biology
Genetic Variation
Molecular Sequence Annotation
Plant
biology.organism_classification
lcsh:Genetics
570 Life sciences
biology
Rice
De novo genome assembly
Reference genome
010606 plant biology & botany
Subjects
Details
- ISSN :
- 14712164
- Database :
- OpenAIRE
- Journal :
- BMC Genomics, 20, BMC Genomics, BMC Genomics, Vol 20, Iss 1, Pp 1-9 (2019), BMC genomics, vol 20, iss 1
- Accession number :
- edsair.doi.dedup.....483ea4d52dcdd703ed500fbaf0b3ec8e