红毛丹基因组中MITEs转座子的鉴定与演化分析

Identification and Evolutionary Analysis of MITE Transposons in Rambutan Genome

【目的】对红毛丹基因组中的MITEs(miniature inverted-repeat transposable elements)转座子进行鉴定、分类和演化分析,为红毛丹基因组注释、演化及相关基因功能等方面的研究提供理论依据和数据基础。【方法】基于生物信息学方法和红毛丹全基因组数据,对MITEs转座子进行鉴定,并系统分析其在宿主基因组中的分类、含量、家族演化关系、扩增模式、分布模式、插入偏好模式及邻近基因的功能。【结果】红毛丹中共鉴定出MITEs转座子588个,包括PIF/Harbinger、Mutator、Ac-mMITE、hAT和Ginger共5种超家族;插入时间分析发现较大规模的MITEs转座“爆发”事件分别发生于1~2、4~5和17~18百万年前,PIF/Harbinger超家族几乎在于每个时期都占据主导地位,而Ac-mMITE在转座“爆发”事件中参与度最低;插入位置分析发现MITEs在基因侧翼区插入数量最多,分别有136和137个,插入基因内部数为35个,其中2个插入了外显子内;密度分布分析发现该转座子插入虽具有分散性,但整体偏好基因密集区;插入偏好分析发现MITEs在基因两侧呈现为5 kb以内某一位点插入数最高,随着与基因距离接近,插入数越低的偏好分布模式;MITEs邻近基因功能富集分析表明,MITEs插入内部基因主要富集在硫代葡萄糖苷、葡糖异硫氰酸盐和S-糖苷的代谢及生物合成过程,而被插入5’端侧翼区的基因主要富集在生殖和发育相关生物过程,且大多数基因与各种蛋白复合物的结合和某些酶的活性相关。【结论】研究结果有助于理解MITEs转座子在红毛丹基因组中的基本特征和演化模式,丰富了红毛丹基因组的注释信息,填补了红毛丹中MITEs转座子研究的空白并为其性状改良等方面的研究带来了新的视角。

[Objective] Identification,classification and evolutionary analysis of the miniature invertedrepeat transposable elements(MITEs)in the rambutan genome were conducted to provide theoretical basis and genomic resources for the study of annotation, evolution and corresponding gene function of the rambutan genome.[Method] Bioinformatic tools and genome-wide data of rambutan were used to identify MITEs and systematically analyze its classification,content,evolution,amplification pattern,distribution pattern,insertion preference pattern, and function of adjacent genes.[Result] There were588 complete MITEs in the rambutan genome,including PIF/Harbinger, Mutator, Ac-mMITE,hAT and Ginger superfamilies.Analysis of insertion time showed that several large transposition "burst" events of MITEs occurred between 1-2,4-5 and 17-18 million years ago(MYA),respectively.The PIF/Harbinger superfamily is dominant in almost every phase, while the Ac-mMITE had the lowest participation in the transposition "burst" events.The insertion position analysis showed that the MITEs were mainly inserted in flanking regions of genes(136 upstream and 137 downstream).35 MITEs inserted into gene regions, and 2 of 35 inserted in exons.The density distribution analysis showed that the MITEs inserted around the genes dispersely.Insertion preference analysis showed that MITEs insertion rate is the highest within 5 kb around the genes,and the closer to the genes,the fewer insertions.Functional enrichment analysis of adjacent genes showed that the inserted genes were mainly enriched in glucosinolates,glucosiso-thiocyanates and S-glucosinolates metabolism and biosynthesis.The genes with MITEs inserted in the 5’-flanking regions were mainly enriched in reproductive and developmental processes,and they were related to the binding of various protein complexes and the activities of some enzymes.[Conclusion] These results contributed to the understanding of the basic characteristics and evolutionary pattern of MITEs in the rambutan genome, enhanced genomic annotation of rambutan genome, filled a gap on the research of MITEs in the rambutan genome, and provided a new perspective for the improvement of the host traits.