Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata).
Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata).
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DOI：
10.1371/journal.pone.0256873
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Mondal S
中科院分区：
文献类型：
--
作者：
Ahmed FF;Hossen MI;Sarkar MAR;Konak JN;Zohra FT;Shoyeb M;Mondal S
RNA 沉默是通过 RNA 干扰 (RNAi) 途径基因家族介导的，即 Dicer-Like (DCL)、Argonaute (AGO) 和 RNA 依赖性 RNA 聚合酶 (RDR) 及其顺式作用调节元件。 RNAi途径还与转录后基因沉默（PTGS）机制直接相关，该途径控制真核生物在生长、发育和应激反应过程中的基因调控。然而，RNAi途径基因家族（例如DCL、AGO和RDR）的全基因组鉴定及其与转录因子相关的调控网络分析尚未在许多水果作物物种中进行研究，包括香蕉（Musa acuminata）。在这项研究中，我们通过综合生物信息学方法对香蕉中的 DCL、AGO 和 RDR 基因进行了计算机全基因组鉴定和表征。基于与香蕉基因组中 RNAi 途径相关的多重序列比对和系统发育树，全基因组分析确定了 3 个 MaDCL、13 个 MaAGO 和 5 个 MaRDR 候选基因。这些基因对应于拟南芥 RNAi 沉默基因。对 MaDCL、MaAGO 和 MaRDR 基因的保守结构域、基序和基因结构（外显子-内含子数量）的分析表明，同一基因家族内具有较高的同质性。基因本体（GO）富集分析表明，已鉴定的 RNAi 基因可能参与 RNA 沉默和相关代谢途径。通过 TF 与候选 RNAi 基因家族之间的网络和子网络分析，鉴定了许多重要的转录因子 (TF)，例如 ERF、Dof、C2H2、TCP、GATA 和 MIKC_MADS 家族。此外，在候选MaDCL、MaAGO和MaRDR基因中鉴定了与光响应（LR）、应激响应（SR）、激素响应（HR）和其他活动（OT）功能相关的顺式作用调控元件。对这些 RNAi 基因家族的全基因组分析提供了与 RNA 沉默相关的有价值的信息，这将有助于进一步表征 RNAi 基因、其调控元件和功能作用，这可能有助于香蕉育种计划的改进。
RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.
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DOI：
10.1038/nrg3355
发表时间：
2013-02
期刊：
Nature reviews. Genetics
影响因子：
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芸苔属物种 Dicer 样、Argonaute 和 RNA 依赖性 RNA 聚合酶基因家族的全基因组鉴定及其拟南芥同源物抗核盘菌的功能分析
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Cao JY;Xu YP;Li W;Li SS;Rahman H;Cai XZ
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10.1038/nrm4085
发表时间：
2015-12
期刊：
Nature reviews. Molecular cell biology
影响因子：
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通讯作者：
Martienssen RA
影响因子：
14.9
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Bailey TL;Johnson J;Grant CE;Noble WS
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