The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Zhigang Hao; Zhiping Zhang; Jinan Zhang; Xiufen Cui; Jianqiang Li; Laixin Luo; Yingbin Li

doi:10.3389/fpls.2024.1362045

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Front Plant Sci. 2024 Mar 6:15:1362045. doi: 10.3389/fpls.2024.1362045. eCollection 2024.

Authors

Zhigang Hao^#^{1

2

3}, Zhiping Zhang^#¹, Jinan Zhang², Xiufen Cui^{3

4}, Jianqiang Li^{3

4}, Laixin Luo^{3

5}, Yingbin Li¹

Affiliations

¹ Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China.
² Sanya Institute of China Agricultural University, Sanya, Hainan, China.
³ Hainan Seed Industry Laboratory, Sanya, Hainan, China.
⁴ Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China.
⁵ MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, China.

^# Contributed equally.

Abstract

Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.

Keywords: Aglaia odorata; MTPT; RNA editing; mitochondrial genome; recombination.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. The research was supported by The Open Fund of State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Grant No: gzkf2022007, Sanya Institute of China Agricultural University (SYND-2022-11), and the Young Talent Project of Yunnan Revitalization Talent Support Program (XDYC-QNRC-2022-0719) and Hainan Seed Industry Laboratory (Grant No: B23C10004).