MITE annotation and landscape in 207 plant genomes reveal their evolutionary dynamics and functional roles

Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements prevalent in eukaryotic genomes, contributing to various genomic and genic functions in plants. However, research on MITEs mainly targets a few species, limiting a comprehensive understanding and systematic comparison of MITEs in plants. Here, we developed a highly sensitive MITE annotation pipeline with a low false positive rate and applied it to 207 high-quality plant genomes. We found over a 20,000-fold variation in MITE copy numbers among species, with Gnetum montanum harboring the most. The Mutator superfamily is widespread, comprising about 41.5%, whereas Tc1/Mariner and PIF/Harbinger superfamilies expanded rapidly in monocots, particularly in Poaceae. The analysis of MITE insertion times revealed an expansion around 30 million years ago (Mya), peaking at 9−10 Mya, with some species showing another ancient, slower expansion. In three representative families, we identifi..., , # Data from: MITE annotation and landscape in 207 plant genomes reveal their evolutionary dynamics and functional roles Dataset DOI: [10.5061/dryad.bg79cnpns](10.5061/dryad.bg79cnpns) ## Description of the data and file structure These are the seed sequences of MITE data derived from the analysis of 207 species, as well as the hairpin and mature sequences of MITE-derived miRNAs. ### Files and variables #### File: MITE_seed_sequence_207genomes.tar.gz **Description:** The seed sequence of MITEs from 207 plant genomes #### File: MITE-derived-miRNA-hairpin.fa **Description:** The hairpin sequences of MITE-derived miRNAs #### File: MITE-derived-miRNA-mature.fa **Description:** The mature sequences of MITE-derived miRNAs ## Code/software Linux, ,微型反向重复转座元件（Miniature inverted-repeat transposable elements，MITEs）是一类短序列非自主型II类转座元件，广泛存在于真核生物基因组中，可参与植物的多种基因组及基因功能。然而当前针对MITEs的研究多聚焦于少数物种，这限制了学界对植物MITEs的全面认知与系统比较。本研究开发了一套灵敏度高、假阳性率低的MITE注释流程，并将其应用于207个高质量植物基因组。研究发现不同物种间MITE拷贝数差异可达两万倍以上，其中买麻藤（Gnetum montanum）的MITE拷贝数最多。Mutator超家族分布最为广泛，占比约41.5%；而Tc1/Mariner与PIF/Harbinger超家族在单子叶植物中扩张迅速，尤以禾本科（Poaceae）为甚。对MITE插入时间的分析显示，其在约3000万年前（Mya）发生过一次扩张，在900万至1000万年前达到峰值，部分物种还存在另一古老且缓慢的扩张事件。在三个代表性科中，我们鉴定出……，，# 数据来源：MITE注释与207个植物基因组中的MITE景观揭示其演化动态与功能角色 数据集DOI: [10.5061/dryad.bg79cnpns](10.5061/dryad.bg79cnpns) ## 数据与文件结构说明 本数据集包含来自207个物种的MITE分析所得种子序列，以及MITE来源的miRNA的发夹结构序列与成熟序列。 ### 文件与变量 #### 文件：MITE_seed_sequence_207genomes.tar.gz **描述：** 来自207个植物基因组的MITE种子序列 #### 文件：MITE-derived-miRNA-hairpin.fa **描述：** MITE来源的miRNA发夹结构序列 #### 文件：MITE-derived-miRNA-mature.fa **描述：** MITE来源的miRNA成熟序列 ## 代码/软件 Linux操作系统