Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia
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DOI：
10.1105/tpc.18.00517
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发表时间：
2018-12-01
期刊：
影响因子：
11.6
通讯作者：
Bartels, Dorothea
中科院分区：
文献类型：
--
作者：
VanBuren, Robert;Wai, Ching Man;Bartels, Dorothea
虽然几个复活植物基因组已被测序，缺乏合适的脱水敏感的外群限制了基因组的见解脱水耐受性的起源。在这里，我们利用了一个比较系统的密切相关的耐干燥（短叶）和敏感（subracemosa）的物种，以确定基因和路径水平的变化与耐干燥性的演变。我们组装的两个高质量的Lindernia基因组在很大程度上是共线的，超过90%的基因是保守的。L. brevidens和L. subracemosa有证据表明，一个古老的，共享的全基因组复制事件，保留的基因有新功能，与干燥特异性表达L。短齿串联基因重复也富含与干燥相关的功能，包括早期光诱导蛋白在L.短齿比较分析了L. brevidens和L. subracemosa支持在早期脱水、干燥和再水化时间过程中广泛的网络重新布线。许多晚期胚胎发生丰富基因在L. brevidens与L.亚总状花序。在L.短齿富含种子特异性和脱落酸相关的顺式调节元件。这些模块包含了大量的种子相关基因，这些基因在脱水敏感的L。亚总状花序。总之，这些发现表明，脱水耐受性是通过基因复制和现有种子脱水途径的网络水平重新布线的组合而进化的。
Although several resurrection plant genomes have been sequenced, the lack of suitable dehydration-sensitive outgroups has limited genomic insights into the origin of desiccation tolerance. Here, we utilized a comparative system of closely related desiccation-tolerant (Lindernia brevidens) and - sensitive (Lindernia subracemosa) species to identify gene- and pathway-level changes associated with the evolution of desiccation tolerance. The two high-quality Lindernia genomes we assembled are largely collinear, and over 90% of genes are conserved. L. brevidens and L. subracemosa have evidence of an ancient, shared whole-genome duplication event, and retained genes have neofunctionalized, with desiccation-specific expression in L. brevidens. Tandem gene duplicates also are enriched in desiccation-associated functions, including a dramatic expansion of early light-induced proteins from 4 to 26 copies in L. brevidens. A comparative differential gene coexpression analysis between L. brevidens and L. subracemosa supports extensive network rewiring across early dehydration, desiccation, and rehydration time courses. Many LATE EMBRYOGENESIS ABUNDANT genes show significantly higher expression in L. brevidens compared with their orthologs in L. subracemosa. Coexpression modules uniquely upregulated during desiccation in L. brevidens are enriched with seed-specific and abscisic acid-associated cis-regulatory elements. These modules contain a wide array of seed-associated genes that have no expression in the desiccation-sensitive L. subracemosa. Together, these findings suggest that desiccation tolerance evolved through a combination of gene duplications and network-level rewiring of existing seed desiccation pathways.