Abstract
BACKGROUND: Basic helix-loop-helix (bHLH) transcription factors regulate plant growth, stress responses, and hormone signaling. Advances in bioinformatics, the bHLH transcription factor family has been comprehensively identified and characterized across a wide range of organisms. However, a genome-wide analysis of this family has not yet been performed in Lilium davidii var. unicolor, an economically important species in China valued for its nutritional and medicinal properties. RESULTS: Using whole-genome sequencing data, we identified 214 LdbHLH genes from the L. davidii var. unicolor genome and classified them into 23 subfamilies based on phylogenetic analysis. Gene structure was highly conserved within subfamilies. Collinearity analysis identified five syntenic gene pairs (LdbHLH3-LdbHLH9, LdbHLH17-LdbHLH61, LdbHLH176-LdbHLH125, LdbHLH181-LdbHLH197, and LdbHLH210-LdbHLH200), all derived from segmental duplication, indicating limited large-scale expansion. Promoter analysis showed that LdbHLH genes commonly contain cis-regulatory elements associated with development, abiotic stress, and hormone responses, suggesting their potential roles in signal crosstalk. Expression profiling demonstrated clear tissue specificity, with certain genes highly expressed in leaves, scales, stems, or tepals. Under hormone and stress treatments, most genes exhibited transient expression changes, while some genes, such as LdbHLH76 under salt stress and LdbHLH7 under ABA treatment, were strongly upregulated. Functional assays further confirmed that LdbHLH12, LdbHLH46, LdbHLH76, and LdbHLH189 positively contribute to salt tolerance. CONCLUSIONS: This study provides the first comprehensive functional and genomic characterization of the bHLH family in L. davidii var. unicolor, offering insights into their roles in stress adaptation and tissue development, and identifying candidate targets for molecular breeding aimed at enhancing stress resilience.
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Claims 10
Claim · model-written summary
Whole-genome data identified 214 LdbHLH genes in the Lilium davidii var. unicolor genome.
- Taxon
- Lilium davidii var. unicolor
Lilium davidii var. unicolort0 - Gene
- LdbHLHe0
- Outcome
- 214 LdbHLH genese0
- Value
- 214e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“we identified 214 LdbHLH genes from the L. davidii var. unicolor genome”
Claim · model-written summary
The LdbHLH genes were classified into 23 subfamilies based on phylogenetic analysis.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Gene
- bHLH gene familyt0
- Outcome
- subfamiliese0
- Value
- 23e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“classified them into 23 subfamilies based on phylogenetic analysis”
Claim · model-written summary
Gene structure of the LdbHLH genes was highly conserved within subfamilies.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Outcome
- Gene structuree0
- Direction
- highly conservede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Gene structure was highly conserved within subfamilies”
Claim · model-written summary
Collinearity analysis identified five syntenic LdbHLH gene pairs, all derived from segmental duplication.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Outcome
- five syntenic gene pairse0
- Qualifier
- all derived from segmental duplicatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Collinearity analysis identified five syntenic gene pairs”
e1“all derived from segmental duplication”
Claim · model-written summary
LdbHLH gene promoters commonly contain cis-regulatory elements associated with development, abiotic stress and hormone responses.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Gene
- LdbHLHe0
- Outcome
- cis-regulatory elementse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“LdbHLH genes commonly contain cis-regulatory elements associated with development, abiotic stress, and hormone responses”
Claim · model-written summary
LdbHLH expression showed clear tissue specificity, with certain genes highly expressed in leaves, scales, stems or tepals.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Organ / stage
- leaves, scales, stems, or tepalse0
- Outcome
- tissue specificitye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Expression profiling demonstrated clear tissue specificity, with certain genes highly expressed in leaves, scales, stems, or tepals”
Claim · model-written summary
Under hormone and stress treatments most LdbHLH genes exhibited transient expression changes.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Treatment
- hormone and stress treatmentse0
- Outcome
- expression changese0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Under hormone and stress treatments, most genes exhibited transient expression changes”
Claim · model-written summary
LdbHLH76 was strongly upregulated under salt stress.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Treatment
- salt stresse0
- Gene
- LdbHLH76e0
- Outcome
- expressione0
- Direction
- strongly upregulatede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Under hormone and stress treatments, most genes exhibited transient expression changes, while some genes, such as LdbHLH76 under salt stress and LdbHLH7 under ABA treatment, were strongly upregulated”
Claim · model-written summary
LdbHLH7 was strongly upregulated under ABA treatment.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Treatment
- ABA treatmente0
- Gene
- LdbHLH7e0
- Outcome
- expressione0
- Direction
- strongly upregulatede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Under hormone and stress treatments, most genes exhibited transient expression changes, while some genes, such as LdbHLH76 under salt stress and LdbHLH7 under ABA treatment, were strongly upregulated”
Claim · model-written summary
Functional assays confirmed that LdbHLH12, LdbHLH46, LdbHLH76 and LdbHLH189 positively contribute to salt tolerance.
- Taxon
- Lilium davidii var. unicolorLilium davidii var. unicolort0
- Gene
- LdbHLH12, LdbHLH46, LdbHLH76, and LdbHLH189e0
- Outcome
- salt tolerancee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“bHLH gene family in Lilium davidii var. unicolor”
e0“Functional assays further confirmed that LdbHLH12, LdbHLH46, LdbHLH76, and LdbHLH189 positively contribute to salt tolerance”