Rong Wan1, Jingran Liu1, Zhengmei Yang1, Panpan Zhu2, Qinghe Cao3, Tao Xu4. 1. 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. 2. Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, South Korea. 3. Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121, Jiangsu, China. 4. 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. xutao_yr@126.com.
Abstract
BACKGROUND: 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. OBJECTIVE: Identification and characterisation of DEAD-box transcription factors in sweet potato wild ancestor I. trifida genome. METHOD: A systematic genome-wide analysis was conducted to identify the DEAD-box transcription factors in the I. trifida genome. RESULTS: 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. CONCLUSION: 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.
BACKGROUND: 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. OBJECTIVE: Identification and characterisation of DEAD-box transcription factors in sweet potato wild ancestor I. trifida genome. METHOD: A systematic genome-wide analysis was conducted to identify the DEAD-box transcription factors in the I. trifida genome. RESULTS: 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. CONCLUSION: 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.