BACKGROUND Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological processes. However, there is no systematic analysis of MADS-box family genes in pineapple (Ananas comosus). RESULTS Forty-eight MADS-box genes were identified in the pineapple genome. Based on the phylogenetic studies, pineapple MADS-box genes can be divided into type I and type II MADS-box genes. Thirty-four pineapple genes were classified as type II MADS-box genes including 32 MIKC-type and 2 Mδ-type, while 14 type I MADS-box genes were further divided into Mα, Mβ and Mγ subgroups. A majority of pineapple MADS-box genes were randomly distributed across 19 chromosomes. RNA-seq expression patterns of MADS-box genes in four different tissues revealed that more genes were highly expressed in flowers, which was confirmed by our quantitative RT-PCR results. There is no FLC and CO orthologs in pineapple. The loss of FLC and CO orthologs in pineapple indicated that modified flowering genes network in this tropical plant compared with Arabidopsis. The expression patterns of MADS-box genes in photosynthetic and non-photosynthetic leaf tissues indicated the potential roles of some MADS-box genes in pineapple CAM photosynthesis. The 23% of pineapple MADS-box genes showed diurnal rhythm, indicating that these MADS-box genes are regulated by circadian clock. CONCLUSIONS MADS-box genes identified in pineapple are closely related to flowering development. Some MADS-box genes are involved in CAM photosynthesis and regulated by the circadian clock. These findings will facilitate research on the development of unusual spiral inflorescences on pineapple fruit and CAM photosynthesis.

中文翻译：

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MADS-box基因的分析揭示了菠萝中开花基因网络的修饰和昼夜表达。

背景技术菠萝是具有CAM光合作用的最重要农作物，但其分子生物学尚未得到充分的研究。MADS-box基因是涉及植物发育和一些生物学过程的关键转录因子。但是，没有对菠萝（Ananas comosus）中MADS-box家族基因的系统分析。结果在菠萝基因组中鉴定出48个MADS-box基因。根据系统发育研究，菠萝MADS-box基因可分为I型和II型MADS-box基因。34个菠萝基因被归为II型MADS-box基因，包括32个MIKC型和2个Mδ-型，而14个I型MADS-box基因又被进一步分为Mα，Mβ和Mγ亚组。大部分菠萝MADS-box基因随机分布在19个染色体上。我们的定量RT-PCR结果证实了MADS-box基因在四种不同组织中的RNA-seq表达模式，表明更多的基因在花中高表达。菠萝中没有FLC和CO直系同源物。菠萝中FLC和CO直系同源物的丢失表明，与拟南芥相比，该热带植物中修饰的开花基因网络。MADS-box基因在光合作用和非光合作用叶片组织中的表达方式表明了某些MADS-box基因在菠萝CAM光合作用中的潜在作用。菠萝MADS-box基因的23％显示昼夜节律，表明这些MADS-box基因受昼夜节律调节。结论在菠萝中鉴定的MADS-box基因与开花发育密切相关。一些MADS-box基因参与CAM光合作用并受昼夜节律调节。这些发现将有助于研究菠萝果实上异常螺旋状花序的发育和CAM的光合作用。