Genomics of the origin and evolution of Citrus

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms (种质), and propose that citrus diversified during the late Miocene epoch (中新世) through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons (季风). A second radiation enabled by migration (迁移) across the Wallace line (华莱士线) gave rise to the Australian limes (酸橙) in the early Pliocene epoch (上新世). Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy (系谱) of major commercial cultivars of citrus. Among mandarins (柑橘) and sweet orange (甜橙), we find an extensive network of relatedness (关联性) that illuminates the domestication of these groups. Widespread pummelo (柚子) admixture among these mandarins and its correlation with fruit size and acidity (酸度) suggests a plausible (貌似有理的) role of pummelo introgression (基因渗入) in the selection of palatable (可口的) mandarins. This work provides a new evolutionary framework for the genus Citrus.

柑橘属，由众多在世界范围内广泛栽培的水果作物组成，其具体包含多少个物种还不确定。本文对十个自然的柑橘属物种进行基因组、系统发育及生物地理方面的研究，研究对象包含60个不同材料的柑橘属物种，覆盖了各种不同的柑橘种质，提出柑橘属物种在中新世晚期由于显著减弱的季风作用而在东南亚快速的辐射。另外一次物种辐射出现在上新世早期，柑橘属物种迁移越过华莱士线，进入澳大利亚，澳大利亚的酸橙由此而来。进一步对于杂种和混合基因组的鉴定和分析揭示了世界上主要栽培种柑橘的谱系。在柑橘和甜橙之间，作者发现一个广泛的关联性网络，揭示了这些群体的驯化作用。在这些柑橘基因组中鉴定到了来自柚子基因组信息，以及其与果实大小和酸度的关系，显示在人为的选择可口的柑橘时，柚子的基因渗入可能扮演着非常重要的作用。本文的工作为柑橘属物种的演化带来了新的提示和参考。

doi: 10.1038/nature25447