摘要
【目的】揭示竹子笋箨的生物学功能与其衰老的分子基础。【方法】利用PacBio Sequel 3代全长转录组测序技术结合生物信息学方法,对孝顺竹不同衰老阶段笋箨全长转录本进行分析。【结果】共获得106148条平均长度为3615 bp的全长转录本。多数转录本长度分布在1.4~7.0 kb。NCBI等注释显示,97.34%的转录本具有注释结果。Mercator注释分析显示笋箨转录本覆盖了其全部34个类别,其中与蛋白类别相关的序列最多,达到了18224条;与microRNA类别相关的最少,仅有9条。在重要功能基因方面,共获得了2489条激素代谢及信号转导相关序列;8804条转录因子序列中393条与光合作用相关的转录本。其中,注释到的189条共30类NAC(NAM/ATAF/CUC)转录因子基因,93.33%的NAC基因,共计28类,其表达量与笋箨衰老呈相关性,包括已被证实在叶片衰老中具有重要调控作用的NAC002、NAC016、NAC017、NAC029(NAP)、NAC042、NAC055与NAC083等7个NAC转录因子与NAC014等14个被报道在叶片衰老中具有潜在作用的NAC基因。NAC025、NAC028、NAC045、NAC061、NAC086、NAC103与NAC1L(NAC 1 Like)7个NAC转录因子表达与孝顺竹笋箨衰老呈正相关,为新发现的正调控笋箨衰老的潜在转录因子。此外,利用MISA程序在76499个序列中检测到简单序列重复(simple sequence repeats,SSR)位点,主要以单核苷酸重复(SSRs)为主,占据了全部(SSRs)的55.2%。利用PLEK等软件共获得2769个长链非编码RNA(long non-coding RNA,lncRNA)。【结论】竹子笋箨基因表达多样化,并具有完整的光合系统基因,显示其具有潜在光合功能;NAC转录因子在孝顺竹笋箨衰老中具有潜在重要调控作用。本研究首次解析了竹子笋箨的全长转录本特征,为今后深入分析竹子笋箨功能及其衰老的分子机制奠定基础。
【Objective】Currently,few reports have described the biological function of the bamboo sheath.This work aimed to elucidate the possible functions and the underlying biological mechanisms of the bamboo sheath from the perspective of molecular biology.【Method】Using PacBio Sequel full-length sequencing technology,we analyzed the transcriptomic profile of the culm sheath at different senescence stages of Bambusa multiplex.【Result】A total of 106148 transcripts with an average length of 3615 base pairs(bp)were obtained.Of those transcripts,97.34%had annotated results.Mercator annotation further revealed that the transcripts covered all 34 functional subgroups associated with the bamboo sheath.The protein subgroup contained the most transcripts,with 18224 transcripts.While the microRNA subgroup contained the least transcripts,with only nine being present in this subgroup.Additionally,2489 hormone-related transcripts and 8804 transcription factors were detected.Interestingly,393 transcripts related to photosynthesis were discovered in the full-length transcriptome of the B.multiplex sheath.A total of 189 transcripts encoding 30 NAC transcription factor genes were also identified.The expression of 93.33%of NAC transcription factor genes was found to be positively or negatively correlated with sheath senescence.Of them,seven NACs,including NAC002,NAC016,NAC017,NAC029(NAP),NAC042,NAC055 and NAC083 have been reported to play important roles in regulating leaf senescence;14 NACs,including NAC014,have been reported to have potential roles in leaf senescence;and seven bamboo sheath senescence-associated NACs,including NAC025,NAC028,NAC045,NAC061,NAC086,NAC103 and NAC1L were newly discovered.The MISA software analysis revealed that 76499 transcripts contain simple sequence repeats(SSRs).Most are single nucleotide repeat SSRs,accounting for 55.2%of all discovered SSRs.Additionally,2769 long non-coding RNAs(lncRNAs)were detected by using software such as PLRK et al.【Conclusion】These results revealed that various gen
作者
鞠烨
江建平
尹增芳
魏强
JU Ye;JIANG Jianping;YIN Zengfang;WEI Qiang(Co-Innovation Center for the Sustainable Forestry in Southern China,Nanjing Forestry University,Nanjing 210037,China;College of Biology and the Environment,Nanjing Forestry University,Nanjing 210037,China;Wanzai Forestry Bureau,Wanzai 336100,China)
出处
《南京林业大学学报（自然科学版）》
CAS
CSCD
北大核心
2020年第6期175-183,共9页
Journal of Nanjing Forestry University：Natural Sciences Edition
基金
国家自然科学基金项目(31670602)
江苏高校“青蓝工程”资助项目
江苏高校优势学科建设工程资助项目(PAPD)。
