摘要
短柄草是温带禾本科植物,因具有基因组小、生长周期短及转化容易等特点,而被推认为温带禾谷类物种的模式植物。比较基因组学研究表明,禾谷类基因组发生了不止一次的全基因组复制。尽管如此,包括短柄草、水稻、高粱和玉米在内的现代禾谷类物种基因组间仍然保持着良好的共线性关系。小分子RNA (small RNA)是一类长18-30nt的单链RNA,在植物的生长发育、逆境响应和维持基因组稳定性方面发挥着重要作用。植物小分子RNA主要分为两类：微RNA(microRNA或miRNA)和小干扰RNA (small interfering RNA或siRNA)。其中miRNA主要在转录后和翻译水平沉默靶mRNA,而24nt siRNA则主要在表观遗传学如DNA甲基化等水平上调节基因的表达。鉴于小分子RNA的重要生物学功能以及短柄草在禾谷类研究中的模式物种地位,本文从短柄草小分子RNA的鉴定、各类小分子RNA的基因组分析以及miRNA在古染色体演化过程中的进化规律等方面开展了以下研究：
一、测定了四个短柄草小分子RNA文库并对它们进行了详细的分析。为发现新的短柄草小分子RNA包括miRNA,我们以营养器官(BdR)、幼穗(BdV)、20小时光照/4小时黑暗生长2周的幼苗(L20h)和8小时光照/16小时黑暗生长2周的幼苗(L8h)为材料构建文库,进行了小分子RNA高通量测序。通过生物信息学分析,在全基因组范围内鉴定了一批miRNA基因、nat-siRNA和phased-siRNA。比较分析发现光周期过程中差异表达的miRNA的功能主要集中在发育(如miR156-160-444)和抗性(miR169-408-1432)方面。除此之外,有些差异表达的siRNA有可能参与光合作用,nat-siRNA则很少参与短柄草的生长发育和光周期过程,而phased-siRNA主要参与花序发育过程。
二、比较了禾谷类物种miRNA的进化规律。为进一步了解miRNA基因家族的特点,本文在基因组范围内将短柄草中鉴定的miRNA基因与其他禾谷类物种中的miRNA进行了比较。首次发现miRNA家族除了通过全基因组复制(WGD)和串联复制进行扩增外,还可以通过转座进行复制。其中串联复制在miRNA基因的扩增中发挥了重要作用,这可能和miRNA基因特殊的发卡结构有关。另外,这些由复制而来的miRNA基因在进化过程中,可以通过成熟miRNA序列的点突变获得新功能。
三、研究了禾谷类古基因组演化中保守miRNA的演变规律。为了研究miRNA基因在WGD后二倍化过程中的演变规律,我们以起源于共同多倍体祖先的短柄草、水稻、高粱和玉米为研究对象,对这些基因组变化中的miRNA演变模式进行了分析。通过全基因组共线性和古复制关系分析,我们发现miRNA基因的产生与丢失(Birth and death)服从基因平衡假说。约有45%的miRNA家族是剂量效应敏感型基因,在二倍化过程中被过保留下来。这些miRNA在亚基因组优势效应下偏好性地分布在古染色体复制对上。同时发现过保留和非过保留miRNA家族的靶基因在功能上有所差异,过保留miRNA家族的靶基因在应答胁迫方面富集,而非过保留miRNA家族的靶基因则主要集中在生物调节等基本生物学过程。
总之,本文通过剖析短柄草小分子RNA的组成及基因组分布,发现了一批与组织特异性和光周期相关的miRNA基因,探索了miRNA基因的扩增机制,初步明确了miRNA的古进化规律,为在短柄草和禾谷类作物中进一步研究miRNA基因的功能提供了基础。
The temperate grass Brachypodium is considered as a promising model of wheat and other energy crops due to its physical and genomic attributes:small genome size, rapid generation time, and highly efficient transformation. As a member of the Pooideae subfamily, Brachypodium shares the same ancetral genome with other grass crops such as rice, sorghum and maize, among which chromosomic synteny and paleo-duplication have been clearly identificated. Small RNAs are single-stranded RNAs of18-30nucleotide (nt) long. They play important roles in plant development, response to various stresses and maintenance of genome stability. There are two major categories of small RNAs in plants, microRNA (miRNA) and small interfering RNA (siRNA). MiRNAs regulate the expression of target genes mainly in the post-transcriptional and translational level, while siRNAs modify genes in epigenetics level. In this PhD dissertation, three aspects of studies were performed surrounding the Brachypodium small RNAs:
1. To identify novel Brachypodium small RNAs (including miRNAs), we sequenced four small RNAs libraries from vegetative tissues, young spikes,8h light/16h dark treated2week old seedlings, and20h light/4h dark treated2week old seedlings. Bioinformatic analaysis identified a number of miRNA genes, nat-siRNAs and phased siRNAs. Some conserved miRNAs exhibited day length-specific expression patterns, mainly involved in development such as miR156-160-444and disease-resistance such as miR169-408-1432. Only a few novel miRNAs were found to be potentially involved in response to day length. The targets of these differential small RNAs were annotated as photosynthesis related genes and hence affect the growth and development of Brachypodium plants. However, a small number of nat-siRNAs were found to be involved in the development and photoperoid process in Brachypodium, while phased-siRNAs may play important roles in the flower development.
2. To further characterize Brachypodium small RNAs in the genome, we performed a genome wide analysis of their structures and family expansion mechanims. We found that, similar to protein-coding genes, the miRNA families were also amplified via transposition in addition to whole genome duplication (WGD), segmental duplication and tandem duplication. Interestingly, tandem duplication seems to significantly contribute to the expansion of miRNA families probably due to their special hairpin structure. Moreover, with the mutation in mature miRNA sequence and the promoter sequences, the duplicated miRNA genes may undergo sub-/neo-functionalization where they may take on novel functions to mke plants better adapt to the environment in the evolution process.
3. Grass species including Brachypodium, rice, sorghum and maize were derived from the same paleo-polyploid ancestor. We conducted a colinearity and paleo-duplication analysis in the genomes of the four grasses, in order to comprehend the evolutionary patterns and their functional evolution. We found that similar to transcript factors, miRNA genes were dosage sensitive, involving in the complicated regulatory network. About45%miRNA gene families were over-retained. This evidence is in support of the gene balance hypothesis that explains gene activities during the genome diploidization process. We found that the distribution of the duplicated miRNAs is biased among ancient chromosome pairs, displaying clear post-WGD subgenome dominance. We also found that, in contrast to the targets of the under-retained miRNA families, which were mainly involved in essential biological regulation processes and metabolic processes, the over-retained miRNA families targets were enriched functions for stress response.
In summary, this work discovered a set of tissue-specific or day length specific miRNAs. It also explores the potential mechanisms for the miRNA family expansion in the grass genomes. Furthermore, the work analyzed the miRNA paleo-evolution patterns, and discovered the subgenome dominance of miRNA genome distribution which provides additional evidence for the gene dosage hypothesis. This work may lay a foundation for further study of miRNA functions in Brachypodium and other grass species.
引文
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