Identification of an NAC Transcription Factor Family by Deep Transcriptome Sequencing in Onion (Allium cepa L.)

Although onion has been used extensively in the past for cytogenetic studies, molecular analysis has been lacking because the availability of genetic resources is limited. NAM, ATAF, and CUC (NAC) transcription factors (TFs) are plant-specific proteins, and they play key roles in plant growth, development, and stress tolerance. However, none of the onion NAC (CepNAC) genes had been identified thus far. In this study, the transcriptome of onion leaves was analyzed by Illumina paired-end sequencing. Approximately 102.9 million clean sequence reads were produced and used for de novo assembly, which generated 117,189 non-redundant transcripts. Of these transcripts, 39,472 were annotated for their function. In order to mine the CepNAC TFs, CepNAC genes were searched from the transcripts assembled, resulting in the identification of all 39 CepNAC genes. These 39 CepNAC proteins were subjected to phylogenetic analysis together with 47 NAC proteins of known function that were previously identified in other species. The results showed that they can be divided into five groups (NAC-I–V). Interestingly, the NAC-IV and -V groups were found to be likely related to the processes of secondary wall synthesis and stress response, respectively. The transcriptome analysis generated a substantial amount of transcripts, which will aid immensely in identifying important genes and accelerating our understanding of onion growth and development. Moreover, the discovery of 39 CepNAC TFs and the identification of the sequence conservation between them and NAC proteins published will provide a basis for further characterization and validation of their functions in the future.

尽管洋葱在过往已被广泛应用于细胞遗传学研究，但受限于遗传资源匮乏，相关分子分析始终存在空白。NAM、ATAF与CUC（NAC）转录因子（TFs）是植物特异性蛋白，在植物生长、发育及胁迫耐受过程中发挥关键调控作用。然而截至目前，尚未有洋葱NAC（CepNAC）基因被成功鉴定。本研究通过Illumina双端测序技术对洋葱叶片转录组进行分析，共获得约1.029亿条清洁序列读段（clean sequence reads），经从头组装得到117189条非冗余转录本，其中39472条获得了功能注释。为挖掘洋葱NAC（CepNAC）转录因子，本研究从组装得到的转录本中检索CepNAC基因，最终成功鉴定出全部39个CepNAC基因。将这39个CepNAC蛋白与此前在其他物种中鉴定出的47个功能已知的NAC蛋白一同进行系统发育分析，结果显示这些蛋白可划分为5个组（NAC-I至V）。值得注意的是，NAC-IV与NAC-V组分别可能与次生细胞壁合成及胁迫响应过程相关。本次转录组分析获得了大量转录本数据，将极大助力重要功能基因的挖掘，并加速我们对洋葱生长发育机制的认知。此外，本研究发现的39个CepNAC转录因子，以及其与已发表NAC蛋白间序列保守性的鉴定结果，将为后续功能表征与验证工作提供重要基础。