Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan
Abstract Background Lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.), and rambutan (Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite the...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06861-8 |
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| author | Suyan Wan Fei Dong Yaying Ma Yuan Yao Yang Wang Yawen Xu Ray Ming Wenping Zhang |
| author_facet | Suyan Wan Fei Dong Yaying Ma Yuan Yao Yang Wang Yawen Xu Ray Ming Wenping Zhang |
| author_sort | Suyan Wan |
| collection | DOAJ |
| description | Abstract Background Lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.), and rambutan (Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. Results We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1. OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors (AGL8, AP3, SHP1, WOX13, LBD1, LBD3, OBP1, SPL2, SPL3, and SPL9) and three genes (IAA8, CSLD5, and CYCD3;2) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. Conclusion We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes. |
| format | Article |
| id | doaj-art-aabd069afd3d4f0b9246feee1382bcf7 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-aabd069afd3d4f0b9246feee1382bcf72025-08-20T04:01:24ZengBMCBMC Plant Biology1471-22292025-07-0125111210.1186/s12870-025-06861-8Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutanSuyan Wan0Fei Dong1Yaying Ma2Yuan Yao3Yang Wang4Yawen Xu5Ray Ming6Wenping Zhang7College of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Life Sciences, College of Future Technology, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversitySchool of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan UniversityAbstract Background Lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.), and rambutan (Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. Results We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1. OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors (AGL8, AP3, SHP1, WOX13, LBD1, LBD3, OBP1, SPL2, SPL3, and SPL9) and three genes (IAA8, CSLD5, and CYCD3;2) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. Conclusion We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes.https://doi.org/10.1186/s12870-025-06861-8SapindaceaeArilTranscriptomeLcLBD1 |
| spellingShingle | Suyan Wan Fei Dong Yaying Ma Yuan Yao Yang Wang Yawen Xu Ray Ming Wenping Zhang Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan BMC Plant Biology Sapindaceae Aril Transcriptome LcLBD1 |
| title | Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan |
| title_full | Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan |
| title_fullStr | Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan |
| title_full_unstemmed | Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan |
| title_short | Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan |
| title_sort | transcriptome analysis provides insights into aril development regulated gene network in lychee longan and rambutan |
| topic | Sapindaceae Aril Transcriptome LcLBD1 |
| url | https://doi.org/10.1186/s12870-025-06861-8 |
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