State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Genome Biol Evol. 2021 Feb 3;13(2). doi: 10.1093/gbe/evaa236.
The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here, we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data. We found that the two subgenomes of the allotetraploids had similar numbers of expressed homeologs, similar percentages of homeologs with dominant expression, and approximately equal numbers of isoforms with alternative splicing, showing an unbiased subgenome evolution as in a few polyploid angiosperms, with a divergence of the two subgenomes at ∼8 Ma. In addition, the nuclear DNA content of the allotetraploid species is almost equal to the sum of two putative progenitors, suggesting limited genome restructuring after allotetraploid speciation. The allopolyploid species of Ephedra might have undergone slow diploidization, and the unbiased subgenome evolution implies that the formation of large genomes in gymnosperms could be attributed to even and slow fractionation following polyploidization.
多倍体基因组的进化动态及其多倍体的后果在被子植物中得到了广泛研究，但在裸子植物中却很少研究。裸子植物麻黄属以多倍体的高频率为特征，因此提供了一个理想的系统来研究异源多倍体基因组的进化模式，并检验裸子植物是否发生了亚基因组优势。在这里，我们对两种麻黄属的异源四倍体物种及其可能的二倍体祖先进行了转录组测序，鉴定了表达的同系物，并基于 PacBio Iso-Seq 和 Illumina RNA-seq 数据分析了可变剪接和同系物表达。我们发现，异源四倍体的两个亚基因组具有相似数量的表达同系物，具有优势表达的同系物的百分比相似，具有可变剪接的同工型数量大致相等，表现出与少数多倍体被子植物相似的无偏亚基因组进化，两个亚基因组在约 8 Ma 时发生分歧。此外，异源四倍体物种的核 DNA 含量几乎等于两个假定祖先的总和，这表明在异源四倍体形成后，基因组的重组有限。麻黄属的异源多倍体可能经历了缓慢的二倍体化，无偏的亚基因组进化表明，裸子植物中大型基因组的形成可能归因于多倍体化后均匀而缓慢的分裂。
