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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1416913
This article is part of the Research Topic Multi-Omics, Genetic Evolution and Crop Domestication View all 6 articles

The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination

Provisionally accepted
Nannan Qin Nannan Qin *Shanjie Yang Shanjie Yang Yunan Wang Yunan Wang Hui Cheng Hui Cheng Yang Gao Yang Gao Xiaojing Cheng Xiaojing Cheng Sen Li Sen Li
  • Shanxi Agricultural University, Jinzhong, China

The final, formatted version of the article will be published soon.

    Introduction: Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. Methods: A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. Results: The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. Conclusion: In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

    Keywords: Lagenaria siceraria, Mitochondrial DNA sequencing, tandem repeats, phylogenetic analysis, RNA editing site

    Received: 13 Apr 2024; Accepted: 24 Jul 2024.

    Copyright: © 2024 Qin, Yang, Wang, Cheng, Gao, Cheng and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Nannan Qin, Shanxi Agricultural University, Jinzhong, China

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