Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics

Area of Science:

• Plant Molecular Biology
• Transcriptomics
• Developmental Biology

Background:

• The genus Gnetum, known for its industrial applications, has poorly understood molecular mechanisms regulating stem development.
• Previous research focused on anatomical structures, leaving molecular pathways largely unexplored.

Purpose of the Study:

• To investigate the molecular mechanisms underlying stem development in Gnetum luofuense.
• To identify key genes and regulatory elements involved in primary and secondary growth stages.

Main Methods:

• Generation of 12 full-length transcriptomes from four stem developmental stages of Gnetum luofuense using Oxford Nanopore Technologies.
• Analysis of alternative splicing (AS), alternative polyadenylation (APA), and long non-coding RNA (lncRNA) expression.
• Application of K-means clustering and weighted gene co-expression network analysis (WGCNA).

Main Results:

• Discovery of 24,151 AS events and 134,391 APA events, with dynamic AS patterns observed, particularly intron retentions.
• Identification of 728 lncRNAs, with a significant increase in cis-regulated target genes.
• Association of primary growth with carbohydrate metabolism and fungi defense, and secondary growth with photosynthesis and nitrogen transport.
• Pinpointing of transcription factors like bHLH, GRF, MYB, AP2/ERF, NAC, PLAZ, and bZIP in distinct growth phases.

Conclusions:

• Nanopore sequencing offers a cost-effective method for generating full-length transcriptome data for seed plant organ development studies.
• This research provides crucial insights into the molecular regulation of Gnetum stem development, highlighting the roles of AS, lncRNAs, and specific transcription factors.