Jeon Donghyun, Kim Changsoo
Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea.
Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea.
Plants (Basel). 2024 Jul 27;13(15):2087. doi: 10.3390/plants13152087.
The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.
十字花科的特点是包含了如卷心菜、西兰花、芥菜和芥末等具有高价值的作物，所有这些作物都以其硫代葡萄糖苷而闻名。在这个科中，许多多倍体物种通过大量的全基因组复制、独立的基因组加倍和杂交事件而分布和形成。该科的进化轨迹以古多倍体化和中多倍体化后多样化的增强和谱系分裂为特征，在其基因组中仍有全基因组复制的明显痕迹。最近的新多倍体化事件显著增加了该科内多倍体物种的比例。尽管对十字花科基因组的测序工作已经很充分，但准确区分亚基因组仍然是一项重大挑战，这常常使组装过程变得复杂。组装策略包括与祖先物种进行比较分析以及检查k-mer、长末端重复反转录转座子和花粉测序。本综述全面探讨了十字花科独特的基因组特征，特别强调了多倍体化事件以及测序和组装的最新策略。本综述将显著提高我们对十字花科多倍体的理解，并有助于未来的基因组组装方法。
