Stitzer Michelle C, Seetharam Arun S, Scheben Armin, Hsu Sheng-Kai, Schulz Aimee J, AuBuchon-Elder Taylor M, El-Walid Mohamed, Ferebee Taylor H, Hale Charles O, La Thuy, Liu Zong-Yan, McMorrow Sarah J, Minx Patrick, Phillips Alyssa R, Syring Michael L, Wrightsman Travis, Zhai Jingjing, Pasquet Rémy, McAllister Christine A, Malcomber Simon T, Traiperm Paweena, Layton Daniel J, Zhong Jinshun, Costich Denise E, Dawe R Kelly, Fengler Kevin, Harris Charlotte, Irelan Zach, Llaca Victor, Parakkal Praveena, Zastrow-Hayes Gina, Woodhouse Margaret R, Cannon Ethalinda K, Portwood John L, Andorf Carson M, Albert Patrice S, Birchler James A, Siepel Adam, Ross-Ibarra Jeffrey, Romay M Cinta, Kellogg Elizabeth A, Buckler Edward S, Hufford Matthew B
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14850 USA.
Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA.
bioRxiv. 2025 Jan 24:2025.01.22.633974. doi: 10.1101/2025.01.22.633974.
Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives and In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.
在过去两千万年里，禾本科黍亚科已经进化到占据全球17%的土地面积。在过去一万年里，这些禾本科植物的驯化产生了我们产量最高的作物，包括玉米、甘蔗和高粱。包括玉米在内的大多数黍亚科物种都显示出多倍体的历史——这种情况虽然提供了多个基因拷贝的进化优势，但对基本细胞过程、基因表达和表观遗传调控构成了挑战。多倍体的基因组研究一直受到多倍体事件频发类群中分类单元抽样不足的限制。在这里，我们展示了来自27个物种的33个基因组组装，包括玉米近缘种的染色体级别组装。在玉米中，多倍体的后续影响已经得到广泛研究，显示出染色体数目减少、重复基因的偏向性分离以及转座元件（TE）扩张。虽然我们在该属内观察到了这些模式，但其他12个多倍体事件却有显著差异。那些四倍体和六倍体保留了较高的染色体数目，维持了几乎完整的重复基因互补，并且只有随机的TE扩增。这些基因组揭示了多倍体的可变结果，挑战了简单预测，并为理解其在一个生态和经济上重要的进化枝中的进化意义提供了基础。
