Qin Nannan, Yang Shanjie, Wang Yunan, Cheng Hui, Gao Yang, Cheng Xiaojing, Li Sen
College of Horticulture, Shanxi Agricultural University, Jinzhong, China.
Department of Development Planning & Cooperation, Shanxi Agricultural University, Taiyuan, China.
Front Plant Sci. 2024 Aug 12;15:1416913. doi: 10.3389/fpls.2024.1416913. eCollection 2024.
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.
A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.
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 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 -2-2-718-223 -391 were successfully verified via PCR amplification and Sanger sequencing.
In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.
葫芦是一种一年生草本植物，不仅具有很高的营养价值和多种药用价值，还被用作西瓜、黄瓜和甜瓜等葫芦科作物嫁接的砧木。细胞器基因组为遗传育种提供了有价值的资源。
采用Illumina和牛津纳米孔技术测序数据的混合策略来组装葫芦线粒体和叶绿体基因组。
葫芦线粒体基因组长度为357547 bp，叶绿体基因组长度为157121 bp。这些基因组有27个同源片段，占葫芦线粒体基因组总长度的6.50%。在线粒体基因组中，鉴定出101个简单序列重复（SSR）和10个串联重复。此外，一对重复序列被证明介导同源重组形成1种主要构象和1种次要构象。通过PCR扩增和Sanger测序验证了这些构象的存在。进化分析表明，葫芦线粒体基因组序列高度保守。此外，共线性分析揭示了葫芦与其近缘种同源片段之间的许多重排。大多数基因的Ka/Ks值在0.3至0.9之间，这意味着葫芦线粒体基因组中的大多数基因处于纯化选择之下。基于长链非编码RNA（lncRNA）序列数据，我们还在38个线粒体蛋白质编码基因（PCG）上共鉴定出589个潜在的RNA编辑位点。通过PCR扩增和Sanger测序成功验证了-2-2-718-223 -391的RNA编辑位点。
总之，我们组装并注释了葫芦线粒体和叶绿体基因组，为类似的细胞器基因组研究提供了理论基础。
