Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize
Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize
复制标题
DOI：
10.1016/j.ygeno.2019.07.009
复制
发表时间：
2020-03-01
期刊：
影响因子：
4.4
通讯作者：
Sekhon, Rajandeep S.
中科院分区：
文献类型：
--
作者：
Bishop, Eugene H.;Kumar, Rohit;Sekhon, Rajandeep S.
AT-钩基序核定位（阿勒）基因具有多种多样但知之甚少的生物学功能。我们鉴定并分析了37个玉米阿勒基因。我们还发现了四个和一个额外的AHL水稻和高粱，分别除了那些先前报道的。玉米AHLs被分为两个进化枝（A和B）和三个不同的类型（I、II和III），如在拟南芥中也报道的。系统发育分析和同源分析表明，虽然阿勒基因家族在植物中的进化分类是保守的，但在玉米中的扩展伴随着新的生物学功能。基因结构分析表明，虽然除一种外，所有I型AHL都缺乏内含子，但II型和III型AHL的起源与内含子的获得相关，这表明进化上不同的时间和空间表达模式，并且很可能是新功能化。基因重复分析表明，玉米AHLs通过分散重复扩增，进一步支持其功能多样性。为了辨别这些功能，我们分析了71个转录组从不同的组织和发育阶段的玉米和AHLs分为8组不同的时间/空间表达谱。共表达分析表明，在胚乳、种子、根、叶和生殖组织特异性网络中有5个AHLs和33个新基因，表明它们在这些器官的发育中起作用。AHLs参与调控的主要过程包括花粉发育、干旱反应、衰老和创伤反应。我们还确定了相互作用的阿勒蛋白共调节重要的过程，包括应激反应。这些对AHLs在植物发育中的作用的新见解为玉米和相关禾本科植物的功能分析提供了平台。
AT-hook motif nuclear localized (AHL) genes have diverse but poorly understood biological functions. We identified and analyzed 37 AHL genes in maize. We also discovered four and one additional AHLs in rice and sorghum, respectively, besides those reported earlier. The maize AHLs were classified into two clades (A and B) and three distinct types (I, II, and III) as also reported in Arabidopsis. Phylogenetic and ortholog analyses showed that, while the evolutionary classification was conserved in plants, expansion of the AHL gene family in maize was accompanied with new biological functions. Gene structure analysis showed that, while all but one Type-I AHLs lacked an intron, origin of Type-II and Type-III AHLs was associated with the gain of introns suggesting evolutionarily distinct temporal and spatial expression patterns and, likely, neofunctionalization. Gene duplication analysis revealed that AHLs in maize expanded via dispersive duplication further supporting their functional diversity. To discern these functions, we analyzed 71 transcriptomes from diverse tissues and developmental stages of maize and classified AHLs into eight groups with distinct temporal/spatial expression profiles. Coexpression analysis implicated 5 AHLs and 33 novel genes in networks specific to endosperm, seed, root, leaf, and reproductive tissues indicating their role in the development of these organs. Major processes coregulated by AHLs include pollen development, drought response, senescence, and wound response. We also identified interactions of AHL proteins in coregulating important processes including stress response. These novel insights into the role of AHLs in plant development provide a platform for functional analyses in maize and related grasses.