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Phytochrome-interacting factors (PIFs) are key transcription factors that regulate plant photomorphogenesis and play important roles in plant growth, development, and responses to environmental stresses. To date, PIF gene family have been identified in many plant species; however, systematic identification and analysis of the PIF gene family in Saccharum spontaneum L., a wild relative of sugarcane, have not yet been reported. In this study, the PIF gene family in S. spontaneum (SsPIF) was identified, and comprehensive analyses were conducted on the physicochemical properties of the encoded proteins,chromosomal localization, intra- and interspecific synteny relationships, and cis-acting elements in promoter regions. In addition, quantitative real-time PCR (qRT-PCR) was used to analyze the expression patterns of SsPIF genes in different tissues of sugarcane and under three plant hormone treatments. The results showed that 12 SsPIF gene were identified from the S. spontaneum genome. These genes encode proteins ranging from 435 to 765 amino acids in length, with molecular weights between 48.14‒83.91 kDa. The predicted isoelectric points (pI) ranged from 5.59 to 6.97; most SsPIF proteins had pI values close to neutral, while a few tended to be acidic or basic. Subcellular localization analysis indicated that all SsPIF proteins are localized in the nucleus. Chromosomal mapping revealed that the SsPIF genes are unevenly distributed across 10 chromosomes. Multiple sequence alignment demonstrated that all SsPIF family members contain conserved basic helix–loop–helix (bHLH) and APB domains, while members of the SsPIF3 subgroup possess a unique APA domain. Comparative synteny analysis showed that fourteen orthologous gene pairs exist between S. spontaneum and rice. Promoter analysis revealed that SsPIF genes are enriched in cis-acting elements related to light responsiveness, hormone signaling, and stress responses. The expression profiles of SsPIF genes exhibited clear tissue specificity, indicating their involvement in the growth and development of S. spontaneum. Furthermore, qRT-PCR analysis revealed distinct expression patterns of the twelve SsPIF genes in response to methyl jasmonate, gibberellin, and auxin treatments. Overall, these findings provide a solid foundation for further functional characterization of the SsPIF gene family and for elucidating their roles in regulating growth, development, and signal transduction pathways in S. spontaneum.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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