盾叶秋海棠基因组微型反向重复转座子MITEs的分布模式和表达分析

Distribution of MITEs (Miniature Inverted-repeat Transposable Elements) and Their Expression Patterns in the Genome of Begonia peltatifolia

摘要:

利用已发表盾叶秋海棠(Begonia peltatifolia)基因组和不同组织的转录组数据，对基因组中微型重复转座子元件(MITEs)进行鉴定和分类，并对其在基因组上的分布特征、插入偏好和表达状态进行了分析。结果表明，共鉴定出925个MITEs拷贝，分属于hAT、Mutator、PIF/Harbinger和Tc1/Mariner等4个超家族，其中hAT家族占比最高，达到70.49%。插入位置分析发现，有59.5%的MITEs元件位于基因侧翼(上下游各5 kb)或基因内，其它约40%的MITEs则位于端粒、着丝粒或其它基因稀疏区域；且位于基因5′侧翼的MITEs拷贝大约是3′侧翼的MITEs的2倍，插入热点在1 000~3 000碱基对距离内，这些共转录的基因主要与次生代谢、能量合成和转运功能有关；插入到基因内部的则主要分布在非编码区(UTRs和内含子)，在外显子上没有观察到MITEs的插入，插入基因功能富集主要与功能、蛋白质合成和遗传信息的表达有关。对盾叶秋海棠不同组织的转录组数据共检测到68次MITEs共转录，在营养器官花梗和叶中极少表达。在生殖器官花和活跃分生组织的根中表达较多，且含有MITEs的转录本中，80.8%和其异构体相比，表达量降低或差别不显著，仅有19.1%的表达量增加。这为开展其耐旱的转座子表观遗传调控机制奠定了基础，为耐旱秋海棠新品种选育提供了基因资源。

Abstract:

By using the published genome of Begonia peltatifolia and the transcriptome data of different tissues, the miniature inverted repeat transposable elements (MITEs) in the genome were identified and classified, and their distribution characteristics, insertion preferences and expression states in the genome were analyzed. The results showed that a total of 925 MITEs copies were identified, belonging to four superfamilies: hAT, Mutator, PIF/Harbinger and Tc1/Mariner, among which the hAT family accounted for the highest proportion, reaching 70.49%. The analysis of insertion positions revealed that 59.5% of the MITEs elements were located in the flanking regions (upstream and downstream 5 kb, respectively) or within genes, while the other approximately 40% of the MITEs were located in telomeres, centromeres or other gene-sparse regions; moreover, the number of MITEs copies located in the 5′ flanking region of genes was approximately twice that in the 3′ flanking region, and the insertion hotspots were within 1000 to 3000 base pairs. These co-transcribed genes were mainly related to secondary metabolism, energy synthesis and transport functions; those inserted into the genes were mainly distributed in non-coding regions (UTRs and introns), and no MITEs insertions were observed in exons. The functional enrichment of the genes with MITEs insertions was mainly related to functions, protein synthesis and the expression of genetic information. A total of 68 MITEs co-transcriptions were detected in the transcriptome data of different tissues of B. peltatifolia, with very little expression in vegetative organs such as pedicels and leaves. They were expressed more in reproductive organs such as flowers and active meristems of roots. Among the transcripts containing MITEs, 80.8% had lower expression levels or no significant difference compared with their isoforms, while only 19.1% had increased expression levels. Therefore, these would lay the foundation for studying the epigenetic regulation mechanism of transposons in drought tolerance and provides genetic resources for the breeding of drought-tolerant Begonia varieties.