【摘 要】
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The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs
【机 构】
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State Key Laboratory of Pharmaceutical Biotechnology,School of Life Sciences,Nanjing University,Nanj
论文部分内容阅读
The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality eval-uation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental pro-cesses.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.
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