草莓属microRNA鉴定及比较基因组学研究

	草莓属microRNA鉴定及比较基因组学研究; Identification and Comparative Genomics Analysis of MicroRNA in Fragaria
	朱楚萌
导师	朱安丹
摘要	MicroRNA is a class of small molecule RNAs with length at 20-24 nt, which has been recently found exerting vital functions in multiple biological processes in plants, such as growth and development, stress response etc. Along with the introduction of next-generation sequencing (NGS) technology, many bioinformatics tools have been developed to predict and identify miRNAs using sRNA-Seq data as input in recent years. However, the effectiveness of these tools for application still lacks of evaluation, due to the complex nature of plant miRNAs. Strawberries are an important horticutural plant, and the cultivars are with high economic values. Besides many cultivars, the genus (Fragaria) also holds rich wild gremplasm resources. As a key factor in epigenetic regulation, miRNA is valuable for crop breeding and trait improvement. Therefore, acquiring the expression profiles of miRNAs in wild strawberry species can provide reference basis for subsequent application studies. In the meanwhile, the genus Fragaria possess abundant ploidy gradients, making it an ideal system for comparative genomics and evolutionary genomics studies. In this study, four tools applicable to plant miRNA identification, miRDeep-P2, Mirnovo, ShortStack and UEA sRNA workbench were first evaluated qualitatively and quantitatively. Here, followed by selecting suitable tool, we took five strawberry wild species for study objects, including diploid Fragaria vesca and Fragaria mandshurica, tetraploid Fragaria orientalis, octoploid Fragaria chiloensis and Fragaria virginiana. With small RNA and degradome sequencing derived from leaf and flower tissues, miRNAs were identifed by de novo prediction at the genome scale, and evolutionary and functional analyses of miRNAs and their target loci were carried out, with the following main results: 1. We systematically evaluated the effectiveness and efficiency of four miRNA identification tools for application in non-model plants, and the results showed that miRDeep-P2 outperformed the other three tools in terms of overall performance, but its identification results were strongly influenced by the mismatch parameter values, and we recommend that it is better to filter false positives in combination with other evidence when identifying miRNAs in non-model plants. 2. We performed genome-wide prediction and homology annotation of miRNAs in five wild species of the genus Fragaria. 79, 87, 120, 118 mature miRNAs were for the first time identified in F. mandshurica, F. orientalis, F. chiloensis and F. virginiana, respectively, and an additional 13 miRNAs candidates were identified in F. vesca based on the integration of previous annotation data. These identified miRNAs seperately contained 15, 26, 36, 38, and 9 unannotated novel miRNAs. 3. Sequence and expression conservation analyses were individually carried out for miRNA precursor and mature sequence, and results showed that: 1) the doubling process of homologous chromosomes may promote the sponta
	2021-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74508
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	朱楚萌. 草莓属microRNA鉴定及比较基因组学研究, Identification and Comparative Genomics Analysis of MicroRNA in Fragaria[D],2021.

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