Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression,Advanced Science

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Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression
Advanced Science ( IF 14.3 ) Pub Date : 2024-04-22 , DOI: 10.1002/advs.202304848
Yingyi Liang ₁ , Jing Hao ₁ , Jieyu Wang ₂ , Guoqiang Zhang ₃ , Yingjuan Su _{4,

5} , Zhong-Jian Liu ₃ , Ting Wang ₁

Affiliation

Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full-length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression-modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra-transcribed region scale. The expMotif-transcribed region combination is the most predominant contributor to the expression-modulating effect of SSRs, and some intra-transcribed regions are critical for this effect. Genes containing the same type of expMotif-SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.

中文翻译：

对兜兰转录组中简单序列重复的统计基因组学分析揭示了调节基因表达的控制旋钮基序

简单序列重复 (SSR) 在基因组中非随机分布，被认为会影响基因表达。基于第一个全长转录组和来自 12 个器官的综合转录组数据集，挖掘并表征了马里波兜兰48 295 个 SSR 的分布模式。统计基因组学分析用于研究转录本中的 SSR 如何影响基因表达。结果证明了 SSR 分布、特征和表达水平之间的相关性。鉴定了九个表达调节基序（expMotifs），并提出了一个模型来解释它们的关键特征、效力和基因功能对转录内区域规模的影响。 expMotif 转录区域组合是 SSR 表达调节作用的最主要贡献者，并且一些内转录区域对于这种作用至关重要。在同一转录区域中包含相同类型的 expMotif-SSR 元件的基因可能在功能、调控或进化方面存在关联。这项研究为理解SSR如何调节基因表达提供了新的证据，并为植物基因工程提供了潜在的调节元件。

更新日期：2024-04-22

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