Genome-Wide Identification and Expression Analysis of the TIM Gene Family in Sea-Island Cotton (Gossypium barbadense) During Fiber Development

The translocase of the inner membrane (TIM) family plays an essential role in mediating the transport of nuclear-encoded precursor proteins across the inner mitochondrial membrane and regulating cellular energy metabolism. Sea-island cotton (Gossypium barbadense) is valued for its superior fiber quality, yet the composition, evolution, and expression patterns of its TIM genes remain unclear. To address this, we performed a genome-wide analysis of the TIM family in G. barbadense, using the diploid cotton G. arboreum, and G. raimondii and the allotetraploid G. hirsutum as comparative references. A total of 44 GbTIM genes were identified in G. barbadense and characterized through phylogenetic, structural, collinearity, promoter, and expression analyses. The TIM family expanded during cotton polyploidization, with tetraploid species containing approximately twice as many genes as diploids. Phylogenetic analysis categorized TIM proteins into seven subfamilies, with Group VI representing the largest clade. Promoter regions were enriched in light- and phytohormone-responsive elements. Interspecific synteny analysis demonstrated extensive collinearity between G. barbadense and its diploid ancestors but limited collinearity with G. hirsutum, indicating divergence among tetraploids. Transcriptomic profiling revealed highly spatiotemporal expression patterns. Gbar_A11G001280 was abundantly expressed during fiber initiation and upregulated in low-lint-percentage germplasm, whereas Gbar_D07G010770 was continuously expressed throughout fiber development. This study clarifies the evolutionary lineage of the TIM family across four cotton species, with a primary focus on G. barbadense, and provides candidate genes for molecular breeding of high-quality fiber. Functional validation of these candidate genes is recommended in future studies.