Plant genomes contain both protein‐coding and noncoding sequences including transposable elements (TEs) and noncoding RNAs (ncRNAs). The ncRNAs are recognized as important elements that play fundamental roles in the structural organization and function of plant genomes. Despite various hypotheses, TEs are believed to be a major precursor of ncRNAs. Transposable elements are also prime factors that cause genomic variation among members of a species. Hence, TEs pose a major challenge in the discovery and analysis of ncRNAs. With the increase in the number of sequenced plant genomes, it is now accepted that a single reference genome is insufficient to represent the complete genomic diversity and contents of a species, and exploring the pan‐genome of a species is critical. In this review, we summarize the recent progress in the field of plant pan‐genomes. We also discuss TEs and their roles in ncRNA biogenesis and present our perspectives on the application of pan‐genomes for the discovery of ncRNAs to fully explore and exploit their biological roles in plants.

中文翻译：

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泛基因组：植物非编码RNA发现的有希望的资源

植物基因组既包含蛋白质编码序列，也包含非编码序列，包括转座因子（TEs）和非编码RNA（ncRNA）。ncRNA被认为是在植物基因组的结构组织和功能中起基本作用的重要元素。尽管有各种假设，但TE被认为是ncRNA的主要前体。转座因子也是导致物种成员之间基因组变异的主要因素。因此，TE在ncRNA的发现和分析中提出了重大挑战。随着测序的植物基因组数量的增加，现在已经公认，单个参考基因组不足以代表物种的完整基因组多样性和含量，因此探索一个物种的全基因组至关重要。在这篇评论中 我们总结了植物全基因组学领域的最新进展。我们还讨论了TE及其在ncRNA生物发生中的作用，并就全基因组在ncRNA发现中的应用提出了观点，以充分探索和利用其在植物中的生物学作用。