Key Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China.
Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, South Korea.
Genes Genomics. 2020 Mar;42(3):325-335. doi: 10.1007/s13258-019-00910-x. Epub 2020 Jan 1.
DEAD-box protein family is the largest subfamily of RNA helicases and plays an important role in RNA metabolism and plant growth, development, and stress responses. Although DEAD-box genes have been characterized in various major crop plants, their identification and characterization in Convolvulaceae is still in infancy. Sweet potato (Ipomoea batatas, in Convolvulaceae) is the seventh most important crop in the world. Ipomoea trifida is one of the ancestors of sweet potato and is an effective resource for sweet potato cross-breeding.
Identification and characterisation of DEAD-box transcription factors in sweet potato wild ancestor I. trifida genome.
A systematic genome-wide analysis was conducted to identify the DEAD-box transcription factors in the I. trifida genome.
We identified 17 ItfDEAD-box genes which distributed unevenly on the nine chromosomes of I. trifida and encoded 29 DEAD transcripts. The phylogenetic analysis classified the DEAD-box proteins into nine groups named I-IX. Homology model prediction of ItfDEAD-box proteins obtained 14 models which lay a preliminary foundation for the further functional exploration of the ItfDEAD-box proteins. The tissue-specific and abiotic stress-responsive expression profiles of ItfDEAD-box genes were analyzed in different tissues and under abiotic stress responses by RNA-seq data and confirmed by quantitative PCR analysis. Some genes were significantly up- or down-regulated by different abiotic stress, suggesting that ItfDEAD-box plays a crucial role in stress responses in I. trifida.
The identification and gene expression of the ItfDEAD-box gene family might shed light on the function exploration of DEAD-box gene in I. trifida and promote the molecular breeding of sweet potato.
DEAD-box 蛋白家族是 RNA 解旋酶中最大的亚家族，在 RNA 代谢以及植物生长、发育和应激反应中发挥着重要作用。尽管已在各种主要作物中鉴定和描述了 DEAD-box 基因，但在旋花科中对其的鉴定和描述仍处于起步阶段。甘薯（Ipomoea batatas，旋花科）是世界上第七大重要作物。Ipomoea trifida 是甘薯的一个祖先，是甘薯杂交的有效资源。
鉴定和描述甘薯野生祖先 Ipomoea trifida 基因组中的 DEAD-box 转录因子。
系统地进行了全基因组分析，以鉴定 I. trifida 基因组中的 DEAD-box 转录因子。
我们鉴定了 17 个 ItfDEAD-box 基因，它们不均匀地分布在 I. trifida 的九条染色体上，并编码了 29 个 DEAD 转录本。系统发育分析将 DEAD-box 蛋白分为九个组，分别命名为 I-IX。ItfDEAD-box 蛋白的同源模型预测获得了 14 个模型，为进一步探索 ItfDEAD-box 蛋白的功能奠定了初步基础。通过 RNA-seq 数据和定量 PCR 分析，分析了不同组织和非生物胁迫响应中 ItfDEAD-box 基因的组织特异性和非生物胁迫响应表达谱。一些基因在不同的非生物胁迫下显著上调或下调，表明 ItfDEAD-box 在 I. trifida 的应激反应中起着关键作用。
ItfDEAD-box 基因家族的鉴定和基因表达可能为 DEAD-box 基因在 I. trifida 中的功能探索提供线索，并促进甘薯的分子育种。
