# Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family in Lilium bakerianum var. rubrum

## TL;DR

This study identifies and analyzes bHLH transcription factors in Lilium bakerianum var. rubrum, revealing their roles in floral development and pigmentation.

## Contribution

First genome-wide identification and expression profiling of bHLH transcription factors in Lilium bakerianum var. rubrum.

## Key findings

- 113 high-confidence bHLH genes were identified and annotated in Lilium bakerianum var. rubrum.
- Phylogenetic analysis grouped the bHLH genes into 13 clades, showing lineage-specific expansions and contractions.
- Expression profiling revealed two transcriptional waves and 17 genes active exclusively during the bud stage, suggesting roles in early floral development.

## Abstract

Background/Objectives: The basic helix–loop–helix (bHLH) transcription factor family regulates plant development, metabolism, and stress responses. Yet, its genome-wide composition remains unexplored in Lilium bakerianum var. rubrum (LBVR), an ornamental lily valued for its floral traits. This study aimed to identify, classify, and profile the bHLH family in LBVR using full-length transcriptomic resources. Methods: PacBio HiFi full-length transcriptome sequencing was combined with Illumina RNA-seq for accurate structural annotation and expression quantification. Candidate bHLHs were identified by iTAK and HMMER-Pfam, and their physicochemical properties, secondary structures, motifs, and phylogenetic positions were examined. Expression patterns were analyzed across four floral stages (bud, initial bloom, full bloom, and late bloom). Results: A total of 113 high-confidence bHLH genes were identified, with ~90% successfully annotated. The proteins displayed variation in molecular weight, isoelectric point, structural features, and motif composition. Phylogenetic analysis placed them into 13 clades consistent with Arabidopsis subfamilies, revealing lineage-specific expansions and contractions. Expression profiling showed that 95 genes were active in at least one stage, with two transcriptional waves: a strong bud-to-initial-bloom activation and a secondary wave spanning anthesis. Seventeen genes were expressed exclusively at the bud stage, suggesting roles in early floral-organ initiation and pigmentation. Conclusions: This work provides the first genome-wide characterization of bHLHs in LBVR. The integrated sequencing approach generated a robust catalogue and developmental expression map, offering candidates for functional studies and resources for breeding in lilies.