Gene content and organization of the oat mitochondrial genome

Siculella, Luisa; Damiano, Fabrizio; Cortese, Maria; Dassisti, E.; Rainaldi, Guglielmo; Gallerani, Raffaele; Benedetto, C. De

doi:10.1007/s001220100568

Cited by 15 publications

(13 citation statements)

References 26 publications

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“…Specifically, Bowtie2 software with the–al-conc flag 33 was applied to map sequence reads to the reference organelle genomes and to extract those mapped sequence reads into a separate FASTQ file. There are no oat organelle genomes sequenced and reported so far 34 . In this analysis, wheat cp genome sequences (GenBank accession: AB042240) 35 and wheat mt genome sequences (GenBank accession: AP008982) 36 were used as reference genomes, as wheat is the most closely related grass species with both cp and mt genome sequences published.…”

Section: Methodsmentioning

confidence: 99%

Oat evolution revealed in the maternal lineages of 25 Avena species

2018

Sci Rep

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Cultivated hexaploid oat has three different sets of nuclear genomes (A, C, D), but its evolutionary history remains elusive. A multiplexed shotgun sequencing procedure was explored to acquire maternal phylogenetic signals from chloroplast and mitochondria genomes of 25 Avena species. Phylogenetic analyses of the acquired organelle SNP data revealed a new maternal pathway towards hexaploids of oat genome evolution involving three diploid species (A. ventricosa, A. canariensis and A. longiglumis) and two tetraploid species (A. insularis and A. agadiriana). Cultivated hexaploid A. sativa acquired its maternal genome from an AC genome tetraploid close to A. insularis. Both AC genome A. insularis and AB genome A. agadiriana obtained a maternal genome from an ancient A, not C, genome diploid close to A. longiglumis. Divergence dating showed the major divergences of C genome species 19.9–21.2 million years ago (Mya), of the oldest A genome A. canariensis 13–15 Mya, and of the clade with hexaploids 8.5–9.5 Mya. These findings not only advance our knowledge on oat genome evolution, but also have implications for oat germplasm conservation and utilization in breeding.

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Section: Methodsmentioning

confidence: 99%

Oat evolution revealed in the maternal lineages of 25 Avena species

2018

Sci Rep

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“…The main chromosome has two pairs of large direct repeats, both active in recombination leading to near equimolar levels of the reference and recombinant genome conformations (Figure 6). This pattern of recombinational equimolarity appears to be the rule for large recombining repeats that have been investigated semiquantitatively in other angiosperm mitochondrial genomes (Palmer and Shields, 1984;Palmer and Herbon, 1986;Stern and Palmer, 1986;Lejeune et al, 1987;Siculella and Palmer, 1988;Folkerts and Hanson, 1989;Coulthart et al, 1990;Siculella et al, 2001;Sloan et al, 2010). By contrast, the 3.6-kb direct repeat on the small cucumber chromosomes occupies a distinctly different recombinational equilibrium, with the split conformation outnumbering the integrated conformation by 9:1 (Figures 5 and 6).…”

Section: Differential Recombinational Equilibria Of Large Repeatsmentioning

confidence: 97%

“…In this case, recombination at one of the direct repeats will simultaneously increase the frequency of the recombinant conformation for itself along with the reference conformation for the other direct repeat (Figure 7), leading to a state of apparent recombinational equimolarity for both pairs of repeats (Figure 7), as seen in the main cucumber chromosome (Figure 6). If correct, this model appears to be specific to this genome because those examined plant mitochondrial genomes which, in their entirety, are analogous to the two smaller cucumber chromosomes in containing but a single pair of large recombining direct repeats (many of them no larger than the 3.6-kb cucumber repeat) appear to be at or near recombinational equimolarity (Palmer and Shields, 1984;Palmer and Herbon, 1986;Stern and Palmer, 1986;Siculella and Palmer, 1988;Siculella et al, 2001). …”

Section: Differential Recombinational Equilibria Of Large Repeatsmentioning

confidence: 99%

Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber

et al. 2011

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Members of the flowering plant family Cucurbitaceae harbor the largest known mitochondrial genomes. Here, we report the 1685-kb mitochondrial genome of cucumber (Cucumis sativus). We help solve a 30-year mystery about the origins of its large size by showing that it mainly reflects the proliferation of dispersed repeats, expansions of existing introns, and the acquisition of sequences from diverse sources, including the cucumber nuclear and chloroplast genomes, viruses, and bacteria. The cucumber genome has a novel structure for plant mitochondria, mapping as three entirely or largely autonomous circular chromosomes (lengths 1556, 84, and 45 kb) that vary in relative abundance over a twofold range. These properties suggest that the three chromosomes replicate independently of one another. The two smaller chromosomes are devoid of known functional genes but nonetheless contain diagnostic mitochondrial features. Paired-end sequencing conflicts reveal differences in recombination dynamics among chromosomes, for which an explanatory model is developed, as well as a large pool of low-frequency genome conformations, many of which may result from asymmetric recombination across intermediate-sized and sometimes highly divergent repeats. These findings highlight the promise of genome sequencing for elucidating the recombinational dynamics of plant mitochondrial genomes.

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“…These not only include the nucleus and chloroplast genomes of the host species itself, but may also include sequences derived from the chloroplast and mitochondrial genomes of other species [ 3 ]. Much of this sequence is large (>1 kb) and repetitive in nature [ 25 ], providing sufficient tracts of homology to promote the highly dynamic recombination evident in plant mitochondrial genomes [ 25 – 27 ]. Indeed, it is the high rates of sequence acquisition/loss and recombination that give plant mitochondrial genomes their reputation for rapid intergenic evolution, leading to low levels of non-genic homology among even closely related species [ 2 , 8 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes

et al. 2015

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BackgroundThe mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).MethodsMitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.ResultsThe G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.ConclusionThese results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1988-0) contains supplementary material, which is available to authorized users.

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Gene content and organization of the oat mitochondrial genome

Cited by 15 publications

References 26 publications

Oat evolution revealed in the maternal lineages of 25 Avena species

Oat evolution revealed in the maternal lineages of 25 Avena species

Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber

Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes

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