Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in <i>Brassica</i>

Yang, Jinghua; Liu, Guodong; Zhao, Na; Chen, Sheng; Liu, Dongyuan; Ma, Weiwei; Hu, Zhongyuan; Zhang, Mingfang

doi:10.1111/plb.12414

Cited by 33 publications

(39 citation statements)

References 51 publications

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“…; Yang et al . ). Generally, variation in mitochondrial genome structure is associated with cytoplasmic male sterility (CMS) and its maintainer lines (Allen et al .…”

Section: Discussionmentioning

confidence: 97%

“…Bootstrap values for all major divergences were high (>90%) on the corresponding nodes (Bayesian and maximum parsimony trees are similar, and therefore not displayed). (Grewe et al 2014;Yang et al 2016). Generally, variation in mitochondrial genome structure is associated with cytoplasmic male sterility (CMS) and its maintainer lines (Allen et al 2007;Tanaka et al 2012;Shearman et al 2014), typically resulting in a CMS-associated gene in the mitochondrion.…”

Section: Discussionmentioning

confidence: 99%

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Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

et al. 2017

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Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D ) and G. arboreum (A ) are the putative contributors to the progenitor of G. hirsutum (AD ), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly. Gossypium raimondii (D ) and G. arboreum (A ) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D ) and 687,482 bp (A ), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D and A mitogenomes with mitogenomes of tetraploid Gossypium species (AD , G. hirsutum; AD , G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A ), G. hirsutum (AD ) and G. barbadense (AD ), while eight regions were specific to G. raimondii (D ). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense. The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution.

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“…; Yang et al . ). Generally, variation in mitochondrial genome structure is associated with cytoplasmic male sterility (CMS) and its maintainer lines (Allen et al .…”

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

et al. 2017

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“…With recombination between these and other repeats, Magnolia mtDNAs contain predominant existence of master conformation along with many other alternative conformations with inversions and/or subcircles. This mtDNA heteroplasmy may potentially provide more genetic materials for evolutionary selection [67], hence conferring on Magnolia some ecological and genetic fitness during its evolution.…”

Section: Repeats and Recombination Ratementioning

confidence: 99%

The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms

et al. 2020

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The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms.Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence. OPEN ACCESS Citation: Dong S, Chen L, Liu Y, Wang Y, Zhang S, Yang L, et al. (2020) The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms. PLoS ONE 15(4): e0231020. https://doi.org/10.

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“…However, it remains unsolved and were supposed also from an unidentified or lost mitotype of B. rapa [19]. The nap mitotype was further judged to be derived from B. oleracea, since it was phylogenetically grouped with botrytis-type and capitata-type B. oleracea [20].…”

Section: Epigenetics and Genomicsmentioning

confidence: 99%

Synchronous dissection of chloroplast and mitochondrial genomes clarifies the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

Qiao

Zhang

Huang³

et al. 2020

Preprint

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Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and the detailed interspecific relationships within Brassica genus remains unresolved and somewhere confused. By synchronous sequencing of both the chloroplast DNA and mitochondrial DNA, the whole Brassica phylogeny and the origination of the predominant nap -type B. napus have been clarified based on a large plant population, which maximally integrated the known Brassica species. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. Different from the monophyletical maternal origin of B. juncea and B. carinata from cam-type B. rapa and B. nigra , respectively, the natural B. napus has multiplex maternal origins. It contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species , thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) have dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The elaborated phylogenetic relationships and overall variation data obtained herein can substantially facilitate to develop novel Brassica germplasms and to improve the Brassica crops.

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Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica

Cited by 33 publications

References 51 publications

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms

Synchronous dissection of chloroplast and mitochondrial genomes clarifies the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

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