Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea.
Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea.
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DOI：
10.1038/s41598-017-11327-5
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发表时间：
2017-09-07
影响因子：
4.6
通讯作者：
Jain M
中科院分区：
文献类型：
--
作者：
Singh VK;Rajkumar MS;Garg R;Jain M
生长素反应因子（ARF）是一类在植物生长发育过程中调控生长素反应的转录因子。虽然ARF基因家族的全基因组分析已经在一些物种中进行，但没有关于鹰嘴豆ARF基因的信息。在这项研究中，我们确定了鹰嘴豆基因组中的28个ARF基因（CaARF）。系统发育分析表明，CaARF可以分为四个不同的群体。重复分析显示，50%的CaARF基因来自重复事件。我们分析了CaARF在不同发育阶段的表达模式。CaARF16.3、CaARF17.1和CaARF17.2在花芽发育初期表达量最高，而CaARF6.2在花芽发育后期表达量最高。此外，CaARF4.2、CaARF9.2、CaARF16.2和CaARF7.1在不同的非生物胁迫条件下表现出差异表达，表明它们在非生物胁迫响应中的作用。CaARF、CaIAA和CaGH 3基因之间的共表达网络分析使我们能够识别与CaARF相关的调节网络中涉及的成分。此外，我们鉴定了靶向CaARF的microRNA和触发靶向CaARF的反式作用siRNA产生的TAS3位点。这里提出的分析提供了ARF家族成员的全面信息，并将有助于阐明其在鹰嘴豆中的确切功能。
Auxin response factors (ARFs) are the transcription factors that regulate auxin responses in various aspects of plant growth and development. Although genome-wide analysis of ARF gene family has been done in some species, no information is available regarding ARF genes in chickpea. In this study, we identified 28 ARF genes (CaARF) in the chickpea genome. Phylogenetic analysis revealed that CaARFs can be divided into four different groups. Duplication analysis revealed that 50% of CaARF genes arose from duplication events. We analyzed expression pattern of CaARFs in various developmental stages. CaARF16.3, CaARF17.1 and CaARF17.2 showed highest expression at initial stages of flower bud development, while CaARF6.2 had higher expression at later stages of flower development. Further, CaARF4.2, CaARF9.2, CaARF16.2 and CaARF7.1 exhibited differential expression under different abiotic stress conditions, suggesting their role in abiotic stress responses. Co-expression network analysis among CaARF, CaIAA and CaGH3 genes enabled us to recognize components involved in the regulatory network associated with CaARFs. Further, we identified microRNAs that target CaARFs and TAS3 locus that trigger production of trans-acting siRNAs targeting CaARFs. The analyses presented here provide comprehensive information on ARF family members and will help in elucidating their exact function in chickpea.
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