Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (<i>Cyperus esculentus</i> L.)

LEA_5 domain-containing proteins constitute a small family of late embryogenesis-abundant proteins that are essential for seed desiccation tolerance and dormancy. However, their roles in non-seed storage organs such as underground tubers are largely unknown. This study presents the first genome-scale analysis of the <i>LEA_5</i> family in tigernut (<i>Cyperus esculentus</i> L.), a Cyperaceae plant producing desiccation-tolerant tubers. Four <i>LEA_5</i> genes identified from the tigernut genome are twice of two present in model plants <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i>. A comparison of 86 members from 34 representative plant species revealed the monogenic origin and lineage-specific family evolution in Poales, which includes the Cyperaceae family. <i>CeLEA5</i> genes belong to four out of five orthogroups identified in this study, i.e., LEA5a, LEA5b, LEA5c, and LEA5d. Whereas LEA5e is specific to eudicots, LEA5b and LEA5d appear to be Poales-specific and LEA5c is confined to families Cyperaceae and Juncaceae. Though no syntenic relationship was observed between <i>CeLEA5</i> genes, comparative genomics analyses indicated that LEA5b and LEA5c are more likely to arise from LEA5a via whole-genome duplication. Additionally, local duplication, especially tandem duplication, also played a role in the family expansion in <i>Juncus effuses</i>, <i>Joinvillea ascendens</i>, and most Poaceae plants examined in this study. Structural variation (e.g., fragment insertion) and expression divergence of <i>LEA_5</i> genes were also observed. Whereas <i>LEA_5</i> genes in <i>A. thaliana</i>, <i>O. sativa</i>, and <i>Zea mays</i> were shown to be preferentially expressed in seeds/embryos, <i>CeLEA5</i> genes have evolved to be predominantly expressed in tubers, exhibiting seed desiccation-like accumulation during tuber maturation. Moreover, <i>CeLEA5</i> orthologs in <i>C. rotundus</i> showed weak expression in various stages of tuber development, which may explain the difference in tuber desiccation tolerance between these two close species. These findings highlight the lineage-specific evolution of the <i>LEA_5</i> family, which facilitates further functional analysis and genetic improvement in tigernut and other species.