Annotation-Based Clustering Reveals Functional Transcript Modules Involved in Stress Response and Metabolic Pathways in Cinnamomum

M. Alp Furan; Gülistan Genli

doi:10.18016/ksutarimdoga.vi.1785969

TR EN

Cinnamomum ’da Stres Yanıtı ve Metabolik Yollarla İlişkili İşlevsel Transkript Modüllerinin Açıklamaya Dayalı Kümeleme ile Belirlenmesi

Öz

Transkriptomun işlevsel mimarisinin ortaya konması, özellikle model organizma olmayan bitki türlerinde moleküler düzenleme ve biyolojik karmaşıklığın anlaşılması açısından büyük önem taşımaktadır. Çoğu transkriptomik çalışma, genellikle ifade düzeyine dayalı karşılaştırmalara odaklanmakta olup, bu yaklaşım daha üst düzey işlevsel organizasyonu gözden kaçırabilmektedir. Bu çalışmanın amacı, ifade düzeyinden bağımsız olarak anotasyon temelli özellikler kullanarak Cinnamomum türlerinin transkriptomunda işlevsel olarak tutarlı gen modüllerini belirlemektir. Bu kapsamda transkriptler, Gen Ontolojisi (GO) terimleri, KEGG yolakları, protein domainleri ve BRITE sınıflandırmalarına dayalı olarak özelliklendirilmiş; ardından temel bileşen analizi (PCA) ve K-ortalamalar yöntemi (K-means, k = 4) ile dört kümeye ayrılmıştır. Elde edilen kümeler stres yanıtı, sinyal iletimi, birincil metabolizma ve ikincil metabolit biyosentezi gibi farklı biyolojik süreçlerde belirgin zenginleşme desenleri sergilemiştir. KEGG yolak zenginleştirme analizi, bu işlevsel modüllerin biyolojik geçerliliğini desteklemiş ve metabolik uzmanlaşma ile adaptif stratejileri vurgulamıştır. Sonuç olarak, anotasyon tabanlı denetimsiz kümeleme yaklaşımı, Cinnamomum transkriptomunun biyolojik olarak anlamlı organizasyonunu ortaya koymada etkili bir yöntem sunmaktadır.

Anahtar Kelimeler

Annotation-Based Clustering Reveals Functional Transcript Modules Involved in Stress Response and Metabolic Pathways in Cinnamomum

Abstract

Deciphering the functional architecture of the transcriptome is essential for understanding molecular regulation and biological complexity, particularly in non-model plant species. Most transcriptomic studies rely primarily on expression-level comparisons, which may overlook higher-order functional organization. Here, we aim to identify functionally coherent transcript modules in Cinnamomum species using an annotation-driven unsupervised clustering framework. Transcripts were characterized using Gene Ontology (GO) terms, KEGG pathways, protein domains, and BRITE classifications, followed by principal component analysis (PCA) for dimensionality reduction and K-means clustering (k = 4). The resulting clusters exhibited distinct functional profiles, including modules enriched in stress response, signal transduction, primary metabolism, and secondary metabolite biosynthesis. KEGG pathway enrichment analysis further supported the biological relevance of these modules, highlighting metabolic specialization and adaptive strategies. Overall, this study demonstrates that annotation-based unsupervised clustering provides an effective alternative to expression-only analyses for revealing biologically meaningful transcript organization in Cinnamomum, with implications for plant functional genomics and chemical biology.

Keywords

References

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Details

Primary Language

English

Subjects

Plant Biotechnology

Journal Section

Research Article

Authors

M. Alp Furan ^*
0000-0002-0171-0405
Türkiye

Gülistan Genli
0000-0002-1271-4479
Türkiye

Early Pub Date

April 11, 2026

Publication Date

-

Submission Date

September 17, 2025

Acceptance Date

January 26, 2026

Published in Issue

Year 2026 Number: Advanced Online Publication

DOI

https://doi.org/10.18016/ksutarimdoga.vi.1785969

IZ

https://izlik.org/JA57AZ72BD

Cite

RIS / Bibtex

APA

Furan, M. A., & Genli, G. (2026). Annotation-Based Clustering Reveals Functional Transcript Modules Involved in Stress Response and Metabolic Pathways in Cinnamomum. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, Advanced Online Publication, 1411-1418. https://doi.org/10.18016/ksutarimdoga.vi.1785969