Murdoch's Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
Division of Plant Sciences and Technology, University of Missouri, Columbia, Missouri, USA.
Plant Genome. 2023 Dec;16(4):e20382. doi: 10.1002/tpg2.20382. Epub 2023 Sep 25.
Complete, gapless telomere-to-telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contiguous, nearly gapless, genome assemblies for two economically important soybean [Glycine max (L.) Merr] cultivars (Williams 82 and Lee). The centromeres were distinctly annotated on all the chromosomes of both assemblies. We further found that the canonical telomeric repeats were present at the telomeres of all chromosomes of both Williams 82 and Lee genomes. A total of 10 chromosomes in Williams 82 and eight in Lee were entirely reconstructed in single contigs without any gap. Using the combination of ab initio prediction, protein homology, and transcriptome evidence, we identified 58,287 and 56,725 protein-coding genes in Williams 82 and Lee, respectively. The genome assemblies and annotations will serve as a valuable resource for studying soybean genomics and genetics and accelerating soybean improvement.
完整无间隙的端粒到端粒染色体组装是全面研究复杂区域（如着丝粒或端粒）结构并消除基因顺序、间距和取向不确定性的前提条件。我们使用互补的基因组学技术和组装算法，为两个经济上重要的大豆[Glycine max (L.) Merr]品种（Williams 82 和 Lee）开发了高度连续、几乎无间隙的近乎完整的基因组组装。两个组装体的所有染色体上都明确标注了着丝粒。我们还发现，Williams 82 和 Lee 基因组的所有染色体的端粒都存在着典型的端粒重复序列。Williams 82 中的 10 条染色体和 Lee 中的 8 条染色体完全被重建为单个连续体，没有任何间隙。通过从头预测、蛋白质同源性和转录组证据的结合，我们分别在 Williams 82 和 Lee 中鉴定出 58287 和 56725 个编码蛋白质的基因。基因组组装和注释将成为研究大豆基因组学和遗传学以及加速大豆改良的宝贵资源。
