Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs in Camellia during floral organ development.
Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs in Camellia during floral organ development.
复制标题
DOI：
10.1093/jxb/erw095
复制
发表时间：
2016-04
影响因子：
6.9
通讯作者：
Heng-fu Yin;Zheng-qi Fan;Xinlei Li;Jiangying Wang;Weixin Liu;Bin Wu;Zhen Ying;Liping Liu;
中科院分区：
文献类型：
--
作者：
Heng-fu Yin;Zheng-qi Fan;Xinlei Li;Jiangying Wang;Weixin Liu;Bin Wu;Zhen Ying;Liping Liu;
在植物中，miRNA 是源自具有发夹结构的单链前体的内源性小 RNA。 miRNA 及其靶标的进化代表了指导基因表达的最动态的回路之一，可能在塑造不同植物器官的发育中发挥基础作用。在这里，我们对杜鹃花的五种器官类型进行了高通量小 RNA 测序，以捕获小非编码 RNA 的空间概况。我们总共获得了超过 2.27 亿条高质量读数，并鉴定了 175 个具有成熟序列和前体序列的 miRNA。我们将 miRNA 与已知的 miRNA 数据库进行比对，并揭示了一些保守的以及“新进化的”miRNA 基因。 12 个 miRNA 被鉴定为茶花属特有的，支持“年轻”miRNA 的谱系特异性扩增方式。通过差异表达分析，我们发现许多 miRNA 在某些器官类型中优先丰富。此外，层次聚类分析揭示了组织特异性 miRNA 的独特表达模式。对雄蕊和心皮特异性 miRNA 亚簇靶标的基因本体富集分析表明，miRNA 靶标调节回路参与许多重要的生物过程，使其能够正确规范和器官发生，例如“DNA 整合”和“果实发育”。此外，关键 miRNA 及其靶基因的定量 PCR 揭示了反相关模式，并揭示了不同花器官中关键 miRNA-靶基因对的功能。总而言之，这项工作提供了有关控制花器官发育的 miRNA 靶点调控的有价值的信息，并揭示了茶花中谱系特异性 miRNA 的进化。
In plants, miRNAs are endogenous small RNAs derived from single-stranded precursors with hairpin structures. The evolution of miRNAs and their targets represents one of the most dynamic circuits directing gene expression, which may play fundamental roles in shaping the development of distinct plant organs. Here we performed high-throughput small RNA sequencing in five organ types of Camellia azalea to capture the spatial profile of small non-coding RNA. In total we obtained >227 million high-quality reads and identified 175 miRNAs with mature and precursor sequences. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as 'newly evolved' miRNA genes. Twelve miRNAs were identified to be specific in the genus Camellia, supporting the lineage-specific manner of expansion of 'young' miRNAs. Through differential expression analysis, we showed that many miRNAs were preferentially abundant in certain organ types. Moreover, hierarchical clustering analysis revealed distinctive expression patterns of tissue-specific miRNAs. Gene Ontology enrichment analysis of targets of stamen- and carpel-specific miRNA subclusters showed that miRNA-target regulatory circuits were involved in many important biological processes, enabling their proper specification and organogenesis, such as 'DNA integration' and 'fruit development'. Further, quantitative PCR of key miRNAs and their target genes revealed anti-correlated patterns, and uncovered the functions of key miRNA-target pairs in different floral organs. Taken together, this work yielded valuable information on miRNA-target regulation in the control of floral organ development and sheds light on the evolution of lineage-specific miRNAs in Camellia.