State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
College of Agriculture, Guangxi University, Nanning 530004, China.
Plant Commun. 2023 Jan 9;4(1):100422. doi: 10.1016/j.xplc.2022.100422. Epub 2022 Aug 11.
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
豆科是被子植物中具有高度生物多样性的一个大科，包含了多种经济上重要的作物和生物固氮研究的模式植物。在一些豆科植物中，多倍化事件已经得到了广泛的研究，但由于缺乏某些豆科基部类群物种的基因组信息，新基因的出现仍然是隐蔽的。紫荆（紫荆属）就是这样的一个物种；它是最早从豆科分化出来的，对于豆科的系统发育研究和新基因预测至关重要。为了促进豆科的基因组研究，我们对紫荆进行了基因组测序，获得了一个 352.84Mb 的基因组，进一步组装成了七个假染色体，预测有 30612 个编码蛋白的基因。与其他豆科基因组相比，紫荆的基因组没有表现出线系特异性的多倍化事件。对 22 种豆科植物和 11 种其他被子植物的进一步系统基因组学分析表明，许多基因家族在豆科植物多样化之前和之后都是谱系特异性的。其中，几十种基因是从基因间区进化而来的候选新基因，因此被视为从头起源的基因。它们在编码序列长度、外显子数量、鸟嘌呤-胞嘧啶含量和组织间表达模式等方面与已建立的基因有显著差异。功能分析表明，许多新基因与天冬酰胺代谢有关。这项研究代表了对豆科新基因进化模式的重要认识进展，并为植物系统基因组学研究提供了有价值的资源。
