美国佐治亚大学R. Kelly Dawe团队完成26个不同玉米基因组的从头组装、注释和比较分析。相关论文于2021年8月6日发表于国际学术期刊《科学》。

研究人员报告了26个玉米近交系的新基因组组装、转录组、注释和甲基化组的情况。在这些不同的基因组中，泛基因的数量超过了103,000个，其中大约三分之一在所有的基因型中发现。结果表明，玉米的古老四倍体特征到今天仍在通过分化而继续退化。在重复阵列上出色的相邻性和中心粒的完整注释揭示了主要细胞学标志的额外变异。

研究人员表明，将结构变异与单核苷酸多态性相结合可以提高定量绘制研究的能力。研究人员还记录了DNA甲基化水平上的变异，并证明非甲基化区域富含有助于表型变异的顺式调控元件。

附：英文原文

Title: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Author: Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood, Ethalinda K. S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe

Issue&Volume: 2021/08/06

Abstract: We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

DOI: 10.1126/science.abg5289

Source: https://science.sciencemag.org/content/373/6555/655