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Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa

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Abstract

Key message

We reported the mitochondrial genome of Ventilago leiocarpa for the first time. Two and one sites lead to the generation of stop and stat codon through editing were verified.

Abstract

Ventilago leiocarpa, a member of the Rhamnaceae family, is frequently utilized in traditional medicine due to the medicinal properties of its roots. In this study, we successfully assembled the mitogenome of V. leiocarpa using both BGI short reads and Nanopore long reads. This mitogenome has a total length of 331,839 bp. The annotated results showed 36 unique protein-coding, 16 tRNA and 3 rRNA genes in this mitogenome. Furthermore, we confirmed the presence of a branched structure through the utilization of long reads mapping, PCR amplification, and Sanger sequencing. Specifically, the ctg1 can form a single circular molecule or combine with ctg4 to form a linear molecule. Likewise, ctg2 can form a single circular molecule or can be connected to ctg4 to form a linear molecule. Subsequently, through a comparative analysis of the mitogenome and cpgenome sequences, we identified ten mitochondrial plastid sequences (MTPTs), including two complete protein-coding genes and five complete tRNA genes. The existence of MTPTs was verified by long reads. Colinear analysis showed that the mitogenomes of Rosales were highly divergent in structure. Finally, we identified 545 RNA editing sites involving 36 protein-coding genes by Deepred-mt. To validate our findings, we conducted PCR amplification and Sanger sequencing, which confirmed the generation of stop codons in atp9-223 and rps10-391, as well as the generation of a start codon in nad4L-2. This project reported the complex structure and RNA editing event of the V. Leiocarpa mitogenome, which will provide valuable information for the study of mitochondrial gene expression.

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Data availability

The mitochondrial genome have been deposited in NCBI with accession number: OQ165322, OQ165323 and OQ165324 with the links (https://www.ncbi.nlm.nih.gov/nuccore/OQ165322), (https://www.ncbi.nlm.nih.gov/nuccore/OQ165323) and (https://www.ncbi.nlm.nih.gov/nuccore/OQ165324). The chloroplast genome have been deposited in NCBI with accession number: OR750851 with the links (https://www.ncbi.nlm.nih.gov/nuccore/OR750851). The raw sequencing data have been deposited in NCBI with accession number: SRR22922730, SRR22922731. All data generated by this study are available at the corresponding author upon reasonable request.

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Funding

This work was supported by Young and Middle-aged Teachers of Universities in Guangxi (No. 2021KY0862), Funding for Key Lab. for Zhuang and Yao pharmaceutical quality biology, Guangxi Science & Technology Normal University (No. GXKSKYPT2021007), Guangxi science and technology program (2021AC19423).

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Authors and Affiliations

  1. College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People’s Republic of China

    Song Guo, Zeyang Li, Chunlian Li, Xianglan Liang & Yiming Qin

  2. Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science and Technology Normal University, Laibin, 546199, People’s Republic of China

    Song Guo, Zeyang Li, Chunlian Li & Yiming Qin

  3. Guangxi Botanical Garden of Medicinal Plants, Nanning, 530010, People’s Republic of China

    Yu Liu

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  1. Song Guo
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  4. Yu Liu
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Contributions

YMQ designed the project. SG assembled the mitogenome, analyzed data and wrote the manuscript. ZYL conducted the phylogenetic analysis. YL, CLL and XLL reviewed the manuscript. All authors read and approved the manuscript.

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Correspondence to Yiming Qin.

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We are licensed to collect the plant of V. leiocarpa from Jinxiu Yao Autonomous County, Guangxi Province, China. The collection complies with relevant institutional, national, and international guidelines and legislation.

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Communicated by Kinya Toriyama.

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Guo, S., Li, Z., Li, C. et al. Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa. Plant Cell Rep 43, 77 (2024). https://doi.org/10.1007/s00299-023-03126-2

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