Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica
Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, ch...
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.988368/full |
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| author | Yan Zhong Runxian Yu Runxian Yu Jingfang Chen Ying Liu Renchao Zhou |
| author_facet | Yan Zhong Runxian Yu Runxian Yu Jingfang Chen Ying Liu Renchao Zhou |
| author_sort | Yan Zhong |
| collection | DOAJ |
| description | Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome. |
| first_indexed | 2024-04-11T20:04:55Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T20:04:55Z |
| publishDate | 2022-09-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-98bd9976dd944071ab91d88b9daedfe12022-12-22T04:05:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-09-011310.3389/fpls.2022.988368988368Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indicaYan Zhong0Runxian Yu1Runxian Yu2Jingfang Chen3Ying Liu4Renchao Zhou5State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, ChinaState Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, ChinaState Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, ChinaMitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome.https://www.frontiersin.org/articles/10.3389/fpls.2022.988368/fullAeginetia indicamitochondrial genomerepeat-mediated recombinationintraspecific variationHGT |
| spellingShingle | Yan Zhong Runxian Yu Runxian Yu Jingfang Chen Ying Liu Renchao Zhou Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica Frontiers in Plant Science Aeginetia indica mitochondrial genome repeat-mediated recombination intraspecific variation HGT |
| title | Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica |
| title_full | Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica |
| title_fullStr | Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica |
| title_full_unstemmed | Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica |
| title_short | Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica |
| title_sort | highly active repeat mediated recombination in the mitogenome of the holoparasitic plant aeginetia indica |
| topic | Aeginetia indica mitochondrial genome repeat-mediated recombination intraspecific variation HGT |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.988368/full |
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