Scholarlink

Background <p>Green jujube (<i>Ziziphus mauritiana</i>) is an economically important fruit tree with exceptional nutritional and medicinal values, particularly in tropical undeveloped regions. Light-harvesting chlorophyll a/b-binding proteins (LHC) holds crucial positions in plant photosystem, which is essential for the climate adaptability of green jujube. Nevertheless, comprehensive genome-wide investigation of <i>LHC</i> family genes have never been full studied in genus Ziziphus.</p> Results <p>Herein, we identified respectively 72 and 72 putative <i>LHC</i> genes both in wild and cultivated green jujube based on the haplotype-resolved chromosome-level genomes. These genes were classified into four subfamilies (LHCa, LHCb, ELIP, and PsbS) according to phylogenetic relationships and conserved domains. Members of each subfamily exhibited similar conserved motifs and gene structures. We predicted five phytohormones- and seven environment factors-related <i>cis</i>-regulatory elements in promoter regions of <i>Zmac-LHC</i> and <i>Zmaw-LHC</i>. Additionally, 60 and 62 miRNAs from jujube (<i>Ziziphus jujuba</i>) were found to target 58 <i>Zmac-LHC</i> and 60 <i>Zmaw-LHC</i> genes, respectively. We also discovered 585 transcription factor binding sites among 42 <i>Zmac-LHC</i> genes, and 472 in 40 <i>Zmaw-LHC</i> genes, including AP2, bHLH, bZIP, Dof, GRAS, and others. The secondary and 3D structures provided insights into their protein characteristics. GO and KEGG enrichment highlighted their roles in light responses, photosynthesis, and energy metabolisms. Expression analysis underscored the predominate roles of <i>ZmacI/II/III/IV-LHC1.1/7</i> and <i>ZmawI/II/III/IV-LHC1.1</i>. Correlated analysis revealed the potential functions of <i>ZmawI-LHC1.1</i> on metabolism, contrasting with <i>ZmacI-LHC1.1</i>. WGCNA results elucidated that candidate regulatory networks of <i>ZmawI-LHC1.1</i> and <i>ZmacI-LHC1.1</i>. Moreover, the evolutionary timetree indicated that the “loss and gain” of <i>LHC</i> genes occurred frequently during the polyploidization and domestication processes of green jujube.</p> Conclusions <p>Finally, this study shed light on the impact of domestication on the composition of gene family in autopolyploid plants based on the haplotype-resolved chromosome-level genomes, and provides a foundation for future genetic experiments targeting candidate factors regulating <i>LHC</i> genes, which could significantly advance research in green jujube which regarded as neglected and underutilized plant species.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Comparative genomics of light harvesting chlorophyll a/b binding protein (LHC) family in green jujube (Ziziphus mauritiana) reveal the effect of domestication based on haplotype-resolved genome

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月30日

查看全文
  • Xudong Zhu,
  • Miaohong Wu,
  • Pengyan Chang,
  • Haiming Li,
  • Shuijin Wu,
  • Huiming Huang,
  • Fan Jiang

摘要

Background

Green jujube (Ziziphus mauritiana) is an economically important fruit tree with exceptional nutritional and medicinal values, particularly in tropical undeveloped regions. Light-harvesting chlorophyll a/b-binding proteins (LHC) holds crucial positions in plant photosystem, which is essential for the climate adaptability of green jujube. Nevertheless, comprehensive genome-wide investigation of LHC family genes have never been full studied in genus Ziziphus.

Results

Herein, we identified respectively 72 and 72 putative LHC genes both in wild and cultivated green jujube based on the haplotype-resolved chromosome-level genomes. These genes were classified into four subfamilies (LHCa, LHCb, ELIP, and PsbS) according to phylogenetic relationships and conserved domains. Members of each subfamily exhibited similar conserved motifs and gene structures. We predicted five phytohormones- and seven environment factors-related cis-regulatory elements in promoter regions of Zmac-LHC and Zmaw-LHC. Additionally, 60 and 62 miRNAs from jujube (Ziziphus jujuba) were found to target 58 Zmac-LHC and 60 Zmaw-LHC genes, respectively. We also discovered 585 transcription factor binding sites among 42 Zmac-LHC genes, and 472 in 40 Zmaw-LHC genes, including AP2, bHLH, bZIP, Dof, GRAS, and others. The secondary and 3D structures provided insights into their protein characteristics. GO and KEGG enrichment highlighted their roles in light responses, photosynthesis, and energy metabolisms. Expression analysis underscored the predominate roles of ZmacI/II/III/IV-LHC1.1/7 and ZmawI/II/III/IV-LHC1.1. Correlated analysis revealed the potential functions of ZmawI-LHC1.1 on metabolism, contrasting with ZmacI-LHC1.1. WGCNA results elucidated that candidate regulatory networks of ZmawI-LHC1.1 and ZmacI-LHC1.1. Moreover, the evolutionary timetree indicated that the “loss and gain” of LHC genes occurred frequently during the polyploidization and domestication processes of green jujube.

Conclusions

Finally, this study shed light on the impact of domestication on the composition of gene family in autopolyploid plants based on the haplotype-resolved chromosome-level genomes, and provides a foundation for future genetic experiments targeting candidate factors regulating LHC genes, which could significantly advance research in green jujube which regarded as neglected and underutilized plant species.