A complete assembly of the rice Nipponbare reference genome. Mol. Plant 16, 1232–1236 (2023). Article CAS PubMed Google Scholar Norris, B. J. & Whan, V. A. A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Res 18, 1282...
The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.doi:10.1038/ncomms15324Huilong DuYing YuYanfei MaQiang GaoChengzhi LiangNat CommunNature CommunicationsDU H, YU Y, MA Y, et al. Sequencing and de novo assembly of a near complete indica ...
The long terminal repeat (LTR) Assembly Index (LAI), which evaluates the contiguity of intergenic and repetitive regions of genome assemblies based on the intactness of LTR retrotransposons (LTR-RTs)21, of the Weining genome assembly was 18.42, which was substantially higher than the LAI values o...
However, whole genome de novo assembly, which involves reconstructing the complete genome sequence of an organism without the use of a reference genome, remains a complex and challenging task. The presence of extensive repetitive sequence and high heterozygosity, especially in polyploid species, ...
Here, we describe a route for de novo domestication and improvement of a wild rice relative—the allotetraploid O. alta (CCDD)—by screening the wild allotetraploid rice inventory, establishing an efficient transformation and genome editing system, generating a high-quality annotated assembly of 24 ...
Fragaria iinumae, a diploid progenitor species of octoploid strawberries, likely occupies a basal position within the genus Fragaria. In this study, we report a near-complete genome assembly of F. iinumae v2.0, totaling 241.14 Mb with a contig N50 o
As in an assembly line, designed breeding goals can be achieved step by step when favorable alleles are pyramided recurrently on the platform. Any rice products that we might design, such as complex traits, breeding lines, and new cultivars, can be developed on the platform. Thus, the HJX...
TIF and RelocaTE report both terminal coordinates of the detected TSD as the insertion site, as revealed in a comparative work of mapping insertions of Tos17 transposon in ttm2 and ttm5 lines of japonica rice cv. Nipponbare [37]. A recent improvement of BWA is BWA-MEM, an alignment ...
(Additional file1: Fig. S1). It is shown that at least one-fourth of the genomes have less than 90% GSA completeness in sharp contrast to their more than 90% completeness of genome assembly, especially for embryophytes (Additional file1: Fig. S1a, c) in which a large number of ...
Specific protein–protein interactions (PPIs) enable biological regulation. However, the evolution of PPI specificity is little understood. Here we trace the evolution of the land-plant growth-regulatory DELLA–SLY1/GID2 PPI, revealing progressive increa