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Background <p>Protein ubiquitination is a critical regulatory mechanism in plants, governing essential biological processes such as growth, development, and the response to stress by mediating the degradation of specific proteins. E3 ubiquitin ligases play a key role in this process. Among them, the <i>Arabidopsis Tóxicos en Levadura</i> (ATL) family of proteins functions as an E3 ubiquitin ligase and plays a critical role in plant growth, development, and stress responses. Sweetpotato (<i>Ipomoea batatas</i> (L.) Lam.), a globally significant food and energy crop, has benefited from genome sequencing, enabling the comprehensive identification and functional analysis of the <i>ATL</i> gene family.</p> Results <p>In this study, we identified 85, 99, and 97 <i>ATL</i> genes in sweetpotato (<i>Ipomoea batatas</i>, 2n = 6x = 90) and its two diploid relatives, <i>Ipomoea trifida</i> and <i>Ipomoea triloba</i> (both 2n = 2x = 30), respectively. Phylogenetic analysis revealed that these <i>ATL</i> genes were clustered into six distinct subgroups. We then systematically studied the <i>ATL</i> gene family, including its physicochemical properties, chromosomal localization, phylogenetic relationships, collinearity, gene structures, promoter <i>cis</i>-elements, protein-protein interaction network, and expression patterns.</p> Conclusions <p>Through a comprehensive genome-wide analysis of <i>ATL</i> genes in sweetpotato and its two diploid relatives, we identified a total of 281 <i>ATL</i> genes from sweetpotato, <i>Ipomoea trifida</i>, and <i>Ipomoea triloba</i>. Subsequently, we performed a systematic bioinformatic analysis of the ATL family. We further examined their expression patterns in response to hormonal and abiotic stress treatments. The analysis revealed that members of the <i>ATL</i> gene family play distinct and crucial roles in hormone signaling and abiotic stress responses within sweetpotato and its two diploid relatives. These findings lay the groundwork for further investigation into the abiotic stress response mechanisms of <i>ATL</i> genes in sweetpotato.</p>

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Genome-wide identification of the ATL gene family and their expression analysis in sweetpotato and its two diploid relatives

  • 期刊论文

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  • 发表日期：

    2026年3月7日

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  • Ruitao Liu,
  • Yinghui Yang,
  • Shaopei Gao,
  • Huan Zhang,
  • Ning Zhao,
  • Shaozhen He,
  • Qingchang Liu,
  • Hong Zhai

摘要

Background

Protein ubiquitination is a critical regulatory mechanism in plants, governing essential biological processes such as growth, development, and the response to stress by mediating the degradation of specific proteins. E3 ubiquitin ligases play a key role in this process. Among them, the Arabidopsis Tóxicos en Levadura (ATL) family of proteins functions as an E3 ubiquitin ligase and plays a critical role in plant growth, development, and stress responses. Sweetpotato (Ipomoea batatas (L.) Lam.), a globally significant food and energy crop, has benefited from genome sequencing, enabling the comprehensive identification and functional analysis of the ATL gene family.

Results

In this study, we identified 85, 99, and 97 ATL genes in sweetpotato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida and Ipomoea triloba (both 2n = 2x = 30), respectively. Phylogenetic analysis revealed that these ATL genes were clustered into six distinct subgroups. We then systematically studied the ATL gene family, including its physicochemical properties, chromosomal localization, phylogenetic relationships, collinearity, gene structures, promoter cis-elements, protein-protein interaction network, and expression patterns.

Conclusions

Through a comprehensive genome-wide analysis of ATL genes in sweetpotato and its two diploid relatives, we identified a total of 281 ATL genes from sweetpotato, Ipomoea trifida, and Ipomoea triloba. Subsequently, we performed a systematic bioinformatic analysis of the ATL family. We further examined their expression patterns in response to hormonal and abiotic stress treatments. The analysis revealed that members of the ATL gene family play distinct and crucial roles in hormone signaling and abiotic stress responses within sweetpotato and its two diploid relatives. These findings lay the groundwork for further investigation into the abiotic stress response mechanisms of ATL genes in sweetpotato.