Data Sheet 10_tRNA gene content, structure, and organization in the flowering plant lineage.pdf

Transfer RNAs (tRNAs) are noncoding RNAs involved in protein biosynthesis and have noncanonical roles in cellular metabolism, such as RNA silencing and the generation of transposable elements. Extensive tRNA gene duplications, modifications to mature tRNAs, and complex secondary and tertiary structures impede tRNA sequencing. As such, a comparative genomic analysis of complete tRNA sets is an alternative to understanding the evolutionary processes that gave rise to the extant tRNA sets. Although the tRNA gene (tDNA) structure and distribution in prokaryotes and eukaryotes, specifically in vertebrates, yeasts, and flies, are well understood, there is little information regarding plants. A detailed and comprehensive analysis and annotation of tDNAs from the genomes of 44 eudicots, 20 monocots, and five other non-eudicot and non-monocot species belonging to the Ceratophyllaceae and the ANA (Amborellales, Nymphaeales, and Austrobaileyales) clade will provide a global picture of plant tDNA structure and organization. Plant genomes exhibit varying numbers of nuclear tDNAs, with only the monocots showing a strong correlation between nuclear tDNA numbers and genome sizes. In contrast, organellar tDNA numbers varied little among the different lineages. A high degree of tDNA duplication in eudicots was detected, whereby most eudicot nuclear genomes (91%) and only a modest percentage of monocot (65%) and ANA nuclear genomes (25%) contained at least one tDNA cluster. Clusters of tRNATyr–tRNASer and tRNAIle genes were found in eudicot and monocot genomes, respectively, while both eudicot and monocot genomes showed clusters of tRNAPro genes. All plant genomes had intron-containing tRNAeMet and tRNATyr genes with modest sequence conservation and a strictly conserved tRNAAla-AGC species. Regulatory elements found upstream (TATA-box and CAA motifs) and downstream (poly(T) signals) of the tDNAs were present in only a fraction of the detected tDNAs. A and B boxes within the tDNA coding region show varying consensus sequences depending on the tRNA isotype and lineage. The chloroplast genomes, but not the mitogenomes, possess relatively conserved tRNA gene organization. These findings reveal differences and patterns acquired by plant genomes throughout evolution and can serve as a foundation for further studies on plant tRNA gene function and regulation.

转运RNA（transfer RNAs, tRNAs）是参与蛋白质生物合成的非编码RNA，同时在细胞代谢中发挥RNA沉默、转座因子生成等非经典功能。大量tRNA基因重复事件、成熟tRNA的修饰以及复杂的二级与三级结构，均为tRNA测序带来了阻碍。因此，对完整tRNA组开展比较基因组分析，是解析驱动现存tRNA组形成的进化过程的可行替代方案。尽管目前对原核生物与真核生物（尤其是脊椎动物、酵母及果蝇）中的tRNA基因（transfer RNA gene, tDNA）结构与分布已有充分认知，但针对植物的相关研究仍十分匮乏。对44种真双子叶植物、20种单子叶植物，以及属于金鱼藻科（Ceratophyllaceae）和ANA演化支（Amborellales, Nymphaeales, Austrobaileyales）的5种其他非真双子叶、非单子叶植物的基因组进行全面细致的tDNA分析与注释，将为阐明植物tDNA的结构与组织形式提供全局视角。植物基因组的细胞核tDNA数量存在显著差异，仅单子叶植物的细胞核tDNA数量与基因组大小呈现显著相关性；与之相反，不同演化支的细胞器tDNA数量差异极小。研究发现真双子叶植物中存在高度的tDNA重复现象：绝大多数真双子叶植物细胞核基因组（91%）携带至少一个tDNA基因簇，而仅有少数单子叶植物（65%）及ANA类群细胞核基因组（25%）符合这一特征。分别在真双子叶与单子叶植物基因组中发现了酪氨酸tRNA（tRNATyr）-丝氨酸tRNA（tRNASer）基因簇与异亮氨酸tRNA（tRNAIle）基因簇，而真双子叶与单子叶植物基因组均存在脯氨酸tRNA（tRNAPro）基因簇。所有植物基因组均包含含内含子的甲硫氨酸起始tRNA（tRNAeMet）与酪氨酸tRNA（tRNATyr）基因，这类基因呈现中等程度的序列保守性；同时存在严格保守的丙氨酸tRNA-AGC（tRNAAla-AGC）类型。在检测到的tDNA中，仅部分携带其上游的调控元件（TATA框与CAA基序）及下游的poly(T)信号。tDNA编码区内的A框与B框的保守序列因tRNA亚型与演化支的不同而存在差异。叶绿体基因组而非线粒体基因组，拥有相对保守的tRNA基因组织形式。本研究结果揭示了植物基因组在演化过程中形成的差异与模式，可为后续植物tRNA基因功能与调控的相关研究奠定基础。