Pan-Genomic Insights into LTP Gene Family Evolution across Diploid Cotton Species

Yanghan Lu^1,2Lishuang Guo^2,3Zhengya Wei^1,2Yujun Li^2,3Yue Zhang^2,3Juyun Zheng^2,4Baohua Wang⁵Zhonghua Zhou^1,2Haodong Chen^2,3*

• ¹Hunan Agricultural University, Changsha, China
• ²Yuelushan laboratory, Changsha, China
• ³Hunan Academy of Agricultural Sciences, Changsha, China
• ⁴Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
• ⁵Nantong University, Nantong, China

Lipid-transfer proteins (LTPs) are a class of small, alkaline proteins that bind to and transport various lipid complexes, including fatty acids, phospholipids, glycolipids, and steroids, between phospholipid bilayers. They are essential for signal transduction, stress tolerance, and plant growth and development. On the basis of pan-genome data, this study successfully identified 107 LTP family members in diploid cotton species, including 45 core genes, 43 variable genes, and 19 specific genes. Synteny and selective pressure analyses of LTP family members across nine diploid cotton genomes clarified the evolutionary relationships of the LTP family in these species. The results from structural variation analysis indicated that although SVs alter gene structure, domains, and cis-acting elements, they do not significantly affect gene expression. Further analysis of the differential expression in cotton ovules and roots at various stages revealed that the expression patterns of the LTP gene family exhibit spatiotemporal specificity. According to these results, the LTP gene family may have a variety of biological roles in the growth and development of different plant organs, including controlling the growth and development of cotton fiber and associated stress reactions. Overall, this study utilized the pan-genome of high-quality diploid cotton species to comprehensively investigate the LTP gene family, revealing both conserved and variable evolutionary patterns across species.pan-genome Moreover, the interspecies variations observed among diploid cotton species provide valuable insights into the diversification and adaptive evolution of the LTP gene family. These findings offer new insights into the evolutionary mechanisms and functional diversity of LTP genes and provide valuable references for understanding their evolutionary and biological roles in cotton.