Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
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http://dx.doi.org/10.1016/j.molp.2021.06.018 | DOI Listing |
Nat Genet
January 2025
Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, China.
Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (T2T-sheep1.
View Article and Find Full Text PDFJ Appl Clin Med Phys
December 2024
Department of Physics and Atmospheric Sciences, Dalhousie University, Halifax, Canada.
Purpose: In radiotherapy, body contour inaccuracies may compromise the delineation of adjacent structures and affect calculated dose. Here, we evaluate the un-editable body contours auto-generated by Ethos versions 1.0 (v1) and 2.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan.
The original 100.3 Mb reference genome for , generated from the wild-type laboratory strain N2, has been crucial for analysis of since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010.
View Article and Find Full Text PDFHortic Res
December 2024
Shandong Mountain Tai Forest Ecosystem National Station, Key Laboratory of Forest Cultivation in the Lower Yellow River, National Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During breeding, we observed diverse floral shapes; however, no available genome for has hindered the widespread identification of genes related to flower morphology. Thus, a telomere-to-telomere (T2T) gap-free genome was generated.
View Article and Find Full Text PDFGigascience
January 2024
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China.
Background: Sandalwood, a prized hemiparasitic plant, is highly sought in the commercial market because of its aromatic core materia. The structure and stability of the genome are instrumental in the rapid adaptation of parasitic plants to their surroundings. However, there is a conspicuous lack of research on the genomic-level adaptive evolution of sandalwood.
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