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牻牛儿苗（牻牛儿苗科）线粒体基因组的复杂性：纳米孔测序揭示叶绿体基因转移和DNA重排

Mitochondrial genome complexity in Erodium stephanianum (Geraniaceae): nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements.

作者信息

Xu Xinchen, Meng Qingfei, Li Na, Zou Zichuan, Yang Haonan, Li Ang, Ge Fusheng, Meng Jian, Ding Zixue

机构信息

Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China.

Southeast University affiliated Xuzhou Central Hospital, Xuzhou, Jiangsu, China.

出版信息

Front Genet. 2025 Jul 15;16:1641368. doi: 10.3389/fgene.2025.1641368. eCollection 2025.

DOI:10.3389/fgene.2025.1641368
PMID:40734707
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12303824/
Abstract

The mitochondrial genome of Erodium stephanianum (Geraniaceae) exhibits remarkable complexity revealed through nanopore sequencing, which has unveiled both chloroplast-to-mitochondrion gene transfer and extensive DNA rearrangements. We collected leaf samples from E. stephanianum in June 2023, subsequently extracting total DNA and sequencing the mitogenome using both Oxford Nanopore and Illumina technologies. The assembly yielded a circular mitochondrial genome of 365,414 base pairs, encompassing 28 unique protein-coding genes, 18 tRNA genes, and 3 rRNA genes. Notably, 55 fragments, totaling 58,305 base pairs, showcased sequence homology between the chloroplast and mitochondrion, indicating substantial gene transfer with implications for evolutionary adaptation. Furthermore, codon usage analysis revealed preferential codon utilization, while microsatellite and repeat sequence analyses identified numerous SSRs and tandem repeats within the mitogenome. Phylogenetic analysis positioned E. stephanianum within the Geraniales order, closely clustering with Geranium maderense. This study highlights the dynamic evolution of mitochondrial genomes in E. stephanianum, emphasizing the significance of interorganellar gene transfer and genome rearrangement.

摘要

通过纳米孔测序揭示，牻牛儿苗科老鹳草（Erodium stephanianum）的线粒体基因组表现出显著的复杂性，该测序揭示了叶绿体到线粒体的基因转移以及广泛的DNA重排。我们于2023年6月采集了老鹳草的叶片样本，随后提取总DNA，并使用牛津纳米孔技术和Illumina技术对线粒体基因组进行测序。组装得到了一个365,414个碱基对的环状线粒体基因组，包含28个独特的蛋白质编码基因、18个tRNA基因和3个rRNA基因。值得注意的是，55个片段，总计58,305个碱基对，显示出叶绿体和线粒体之间的序列同源性，表明大量的基因转移对进化适应具有影响。此外，密码子使用分析揭示了优先密码子利用情况，而微卫星和重复序列分析在该线粒体基因组中鉴定出许多简单序列重复（SSRs）和串联重复。系统发育分析将老鹳草置于牻牛儿苗目内，与马德拉天竺葵（Geranium maderense）紧密聚类。这项研究突出了老鹳草线粒体基因组的动态进化，强调了细胞器间基因转移和基因组重排的重要性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/0185ca2b362e/fgene-16-1641368-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/b77138e76168/fgene-16-1641368-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/85c01a796913/fgene-16-1641368-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/7e8f2bb2d983/fgene-16-1641368-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/922b4f0f32ae/fgene-16-1641368-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/7107ea685da2/fgene-16-1641368-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/056aa7f87a55/fgene-16-1641368-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/b237669a1086/fgene-16-1641368-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/9778f084e123/fgene-16-1641368-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/0185ca2b362e/fgene-16-1641368-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/b77138e76168/fgene-16-1641368-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/85c01a796913/fgene-16-1641368-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/7e8f2bb2d983/fgene-16-1641368-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/922b4f0f32ae/fgene-16-1641368-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/7107ea685da2/fgene-16-1641368-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/056aa7f87a55/fgene-16-1641368-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/b237669a1086/fgene-16-1641368-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/9778f084e123/fgene-16-1641368-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f25f/12303824/0185ca2b362e/fgene-16-1641368-g009.jpg

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