Codon usage pattern analysis of Gnetum luofuense (Gnetales) based on transcriptome data. (9th September 2020)

• Record Type: Journal Article
• Authors: Deng, Nan; Liu, Caixia; Song, Qingan; Yao, Min; Yang, Rui; Ma, Fengfeng; Tian, Yuxin
• Is Part Of: Agronomy Journal. Volume 113:Number 2(2021)
• Page Start: 696
• Page End: 705
• Publication Date: 2020-09-09
• Subjects: Agronomy -- Periodicals; 630
• DOI: 10.1002/agj2.20383
• Languages: English
• ISSNs: 0002-1962

Abstract

Abstract: The Gnetum genus is an important medical, grain, and oil crop with ambiguous phylogenetic placement in seed plants. In the current study, full‐length transcripts from G. luofuense L. leaves were utilized for codon usage pattern analysis. For this, a total of 30, 666 full‐length transcripts were used for analysis after data filtering. The GC content of all transcripts was 44.75%, with GC1 being the highest at 50.98%. Eighteen codons were identified as optimal codons, and 16 codons ending with A/U, indicating a higher frequency of A/T codon usage. Advanced analyses indicated that other factors, such as natural selection, play an important role in shaping the codon usage patterns in Gnetum . This study will be beneficial for understanding both the evolutionary mechanisms as well as the history of Gnetum genus. Core Ideas: The GC content of novel and known transcripts are different with average of 44.75%. A/U‐ending codons are preferred in G. luofuense genome. Formation of G.luofuense CUB was dominated by natural selection.