背景:沙漠极其恶劣的环境每时每刻都在发生巨大变化,短期的快速适应性应激反应需要巨大的能量消耗来动员广泛的监管网络,这对沙漠植物本身的生存更加不利。沙丘芦苇,适应了具有复杂多变的生态因子的沙漠环境,是研究禾本科植物在自然状态下响应沙漠组合胁迫的分子机制的理想植物类型。但到目前为止,芦苇遗传资源的数据仍然很少,因此,他们的研究大多集中在生态和生理研究上。
结果:在这项研究中,我们获得了沼泽芦苇(SR)的第一个从头非冗余全长非嵌合(FLNC)转录组数据库,沙丘芦苇(DR)和所有芦苇(合并了SR和DR的等序列数据),使用PacBioIso-Seq技术,并结合Iso-Seq3和Cogent等工具。然后我们鉴定并描述了长链非编码RNA(LncRNA),基于转录组数据库的芦苇中的转录因子(TF)和可变剪接(AS)事件。同时,我们首次在基于UniTransModels的芦苇中鉴定并开发了大量表达序列标签-SSR(EST-SSRs)标记的候选物。此外,通过野生型和同质培养物的差异基因表达分析,我们在沙丘芦苇中发现了大量可能与沙漠胁迫耐受性有关的转录因子,并揭示了Lhc家族的成员在沙丘芦苇对沙漠环境的长期适应中发挥着重要作用。
结论:我们的研究结果为芦苇提供了一个具有广泛适应性和抗性的积极和可用的遗传资源,并为随后的芦苇基因组注释和功能基因组研究提供遗传数据库。
BACKGROUND: The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies.
RESULTS: In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments.
CONCLUSIONS: Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.