The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides

Yu, Runxian; Sun, Chenyu; Zhong, Yan; Liu, Ying; Sanchez‐Puerta, M. Virginia; Mower, Jeffrey P.; Zhou, Renchao

doi:10.1016/j.cub.2021.11.053

Cited by 40 publications

(46 citation statements)

References 83 publications

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“…Parasitic plants also show deeply altered nuclear genome architecture, such as genome size expansion (>100 Gb in Viscum ) ( Marie and Brown, 1993 ), substantial gene loss ( Cuscuta and Sapria ) ( Sun et al., 2018 ; Cai et al., 2021 ) and frequent horizontal gene transfer (HGT) from their hosts ( Kado and Innan, 2018 ). Although rarely characterized, mitogenomes of some parasitic plants also show unusual features, such as minicircular chromosomes ( Yu et al., 2022 ), extreme size reduction, gene loss and high substitution rate ( Skippington et al., 2015 ); extreme heteroplasmy ( Yu et al., 2022 ), and rampant HGT ( Petersen et al., 2020 ). However, these unusual features are not universal to parasitic plants, for example, the hemi-parasitic plant Castilleja paramensis appears to have a mitogenome typical of flowering plants ( Fan et al., 2016 ), and mitochondrial substitution rates of parasitic plants are not always higher than those of non-parasitic plants ( Zervas et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica

Zhong

Chen

et al. 2022

Front. Plant Sci.

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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.

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Section: Introductionmentioning

confidence: 99%

Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica

Zhong

Chen

et al. 2022

Front. Plant Sci.

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“…However, the number of plastid genes is not larger than that of mitochondrial genes in some plants. In some non-photosynthetic plants, such as Hypopitys monotropa 26 or Rhopalocnemis phalloides 27 , the plastomes showed considerable gene loss and size reduction. The plastome size decreases up to 110–200 kb in autotrophic plants 28 .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp.

Yue

et al. 2022

Sci Rep

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Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.

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“…However, dozens of the “empty” chromosomes in the Silene multi-chromosomal mitogenomes exhibit no protein-coding capability. Recently, the mitogenome of another holoparasitic plant, Rhopalocnemis phalloides , has been reported to consist of 21 minicircular chromosomes ranging from 4.95 to 7.86 kb with a shared region containing the replication origin, and replicates via a rolling circle mechanism ( Yu et al, 2022 ). With extensive sampling of Silene noctiflora from 24 different populations, Wu and Sloan predicted that the dominating pattern of the multi-chromosomal variations should be the chromosome loss events after large ancestral expansions ( Wu and Sloan, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Bi¹,

Qu²,

Hou³

et al. 2022

Front. Plant Sci.

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Mitochondria, inherited maternally, are energy metabolism organelles that generate most of the chemical energy needed to power cellular various biochemical reactions. Deciphering mitochondrial genome (mitogenome) is important for elucidating vital activities of species. The complete chloroplast (cp) and nuclear genome sequences of Populus simonii (P. simonii) have been reported, but there has been little progress in its mitogenome. Here, we assemble the complete P. simonii mitogenome into three circular-mapping molecules (lengths 312.5, 283, and 186 kb) with the total length of 781.5 kb. All three molecules of the P. simonii mitogenome had protein-coding capability. Whole-genome alignment analyses of four Populus species revealed the fission of poplar mitogenome in P. simonii. Comparative repeat analyses of four Populus mitogenomes showed that there were no repeats longer than 350 bp in Populus mitogenomes, contributing to the stability of genome sizes and gene contents in the genus Populus. As the first reported multi-circular mitogenome in Populus, this study of P. simonii mitogenome are imperative for better elucidating their biological functions, replication and recombination mechanisms, and their unique evolutionary trajectories in Populus.

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The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides

Cited by 40 publications

References 83 publications

Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica

Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica

Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp.

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

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