Mitochondrial genome structure of rice suspension culture from cytoplasmic male-sterile line (A-58CMS): reappraisal of the master circle

Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework

Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.

Organization of repetitive DNAs and the genomic regions carrying ribosomal RNA, cob, and atp9 genes in the cucurbit mitochondrial genomes

Plants in the genus Cucumis (cucumber and melon) have the largest mitochondrial genomes known among all plants, due in part to the accumulation of repetitive DNAs of varying complexities. Recombination among these repetitive DNAs should produce highly rearranged mitochondrial genomes relative to the smaller mitochondrial genomes of related plants. We cloned and sequenced mitochondrial genomic regions near the rRNA, atp9 and cob genes from cucumber, melon, squash and watermelon (all members of the Cucurbitaceae family), and compared to the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugar beet to study the distribution and arrangement of coding and repetitive DNAs. Cucumber and melon had regions of concentrated repetitive DNAs spread throughout the sequenced regions; few repetitive DNAs were revealed in the mitochondrial genomes of A. thaliana, sugar beet, squash and watermelon. Recombination among these repetitive DNAs most likely produced unique arrangements of the rrn18 and rrn5 genes in the genus Cucumis. Cucumber mitochondrial DNA had more pockets of dispersed direct and inverted repeats than melon and the other plants, and we did not reveal repetitive sequences significantly contributing to mitochondrial genome expansion in both cucumber and melon.

Phylogenetic relationships in the genus Oryza based on mitochondrial RFLPs

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease, EcoRI. RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP. A total of 66 bands were obtained from all of the accessions. The total number of fragments per plant was higher in diploid A-genome species (an average of 35.3) than that in diploid B- and C-genome species and allotetraploid BC- and CD-genome species (an average of 28.2). The extent of the polymorphism in the RFLP patterns was various depending on the probes used. A diverse polymorphism was observed with most of the probes used, i.e. the cob, cox I, atp6, rrn18, rrn26 and atp9 regions, whereas, no polymorphic band was observed with a probe for the coxII region. The genus Oryza was separated into two large clusters. One cluster was comprised of A-genome species and the other cluster was comprised of B-, BC-, C-, and CD- genome species. Within A-genome species, the genetic variation was relatively high. Even in O. sativa species, the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used. However, there was no polymorphism between O. glaberrima and O. barthii. Within the genomes of B, BC, C, and CD, RFLP patterns were similar to each other and they showed a closer affinity except for O. minuta (BBCC). Within the BC genome species, the patterns of O. punctata and O. minuta were largely different from each other and separated into two different subclusters. Thus, the mitochondrial genomes of the two BC species (O. punctata and O. minuta) apparently evolved independently. Among CD genome species (O. latifolia and O. alta), the patterns of one accession, O. alta W0017 were largely different from those of the other accessions of CD genome species.

Organization and expression of the mitochondrial genome in the Nicotiana sylvestris CMSII mutant

Previous analyses suggested that the Nicotiana sylvestris CMSII mutant carried a large deletion in its mitochondrial genome. Here, we show by cosmid mapping that the deletion is 60 kb in length and contains several mitochondrial genes or ORFs, including the complex I nad7 gene. However, due to the presence of large duplications in the progenitor mitochondrial genome, the only unique gene that appears to be deleted is nad7. RNA gel blot data confirm the absence of nad7 expression, strongly suggesting that the molecular basis for the CMSII abnormal phenotype, poor growth and male sterility, is the altered complex I structure. The CMSII mitochondrial genome appears to consist essentially of one of two subgenomes resulting from recombination between direct short repeats. In the progenitor mitochondrial genome both recombination products are detected by PCR and, reciprocally, the parental fragments are detected at the substoichiometric level in the mutant. The CMSII mtDNA organization has been maintained through six sexual generations.

High-frequency inter-parental recombination between mitochondrial genomes of rice cybrids

Analyzing more than 100 independent rice cybrids, we found evidence for inter-molecular recombination between parental mitochondrial genomes occurring at high frequency soon after protoplast fusion. The structure of the region around the atp6 gene showed extensive polymorphism among Indica (MTC-5A), Japonica (Nipponbare), and wild abortive (IR58024A) mitochondrial genomes. Recombination between the mitochondrial genomes of IR58024A and MTC-5A around the atp6 gene was detected by Southern-blot analysis of cybrid plants. Such recombinant mitochondrial molecules were also cloned from IR58024A/Nipponbare cybrid callus. PCR analysis around the atp6 gene demonstrated that inter-parental recombination occurs in practically all cybrid calli within 2 weeks after protoplast fusion. At this point, parental and recombinant mitochondrial genomes co-existed within the callus. Over the course of further cultivation, however, mitochondrial genome diversity decreased as parental and/or recombinant genomes segregated out.

Organization of the mitochondrial Cob 2 pseudogene in different lines of rice

In the fertile rice line IR 36 there are two copies of the apocytochrome b (cob) gene: a functional copy, cob 1, and a pseudogene, cob 2 (Kaleikau et al. 1992). In a survey of diverse rice lines, we found that cob 2 was absent in the wild abortive(WA)-type cytoplasmic male-sterile cytoplasm, but was present in the fertile lines. While cob 1 was conserved among all the lines, fertile and sterile, the cob 2 region was different in the fertile lines tested. The 5' regions of most cob 2 loci were similar to cob 1 (about 4 kb of the flanking region and most of the coding region), but the 3' region varied among different fertile lines. The point of divergence, the break-point, from the cob 1 sequence was conserved in all the cob 2 regions tested. In all the cob 2 regions, this break-point seems to be linked to the variable region of cob 2 through a conserved 192-bp segment, which is not a part of cob 1. It is proposed that the cob 2 regions could have been produced by recombination or insertion events involving cob 1 and the 192-bp segment which is present at different locations in the mitochondrial genomes of the various rice lines.

Pulsed-field gel mapping of maize mitochondrial chromosomes

Pulsed-field gel electrophoresis (PFGE) in combination with infrequently cutting restriction enzymes was used to investigate the structure of the mitochondrial (mt) genome of the maize variety Black Mexican Sweet (BMS). The mt genome of this variety was found to resemble that of the closely related B37N variety, with one recombination and five insertion/deletion events being sufficient to account for the differences observed between the two genomes. The majority of the BMS genome is organized as a number of subgenomic chromosomes with circular restriction maps. Several large repeated sequences are found in the BMS mt genome, but not all appear to be in recombinational equilibrium. No molecules large enough to contain the entire mt genome were discernible using these techniques. The mapping approach described here provides a means of quickly analyzing the large and complex mt genomes of plants.

Polymorphism for ribosomal RNA gene arrangement in the mitochondrial genome of fall rye (Secale cereale L.)

A restriction-fragment-length polymorphism (RFLP) in mitochondrial DNA (mtDNA) was detected between varieties of fall rye (Secale cereale L.) by Southern hybridization with rrn18, the gene encoding the mitochondrial 18S ribosomal RNA. Restriction mapping showed that the RFLP is based on differing numbers of genomic contexts (one vs three) for a recombining-repeat element (the "18S/5S repeat"). From examination of other Secale species, we conclude that the one-context state arose relatively recently, putatively by deletion of two of an ancestral set of three distinct genomic loci containing the mitochondrial 18S/5S repeat. This is consistent with our earlier conclusion that the 18S/5S repeat has probably existed in at least two genomic copies throughout much of the history of the grass family (at least 40 million years). Interestingly, the intervarietal difference in the number of distinct rrn18 loci is not accompanied by a major difference in the number of rrn18 copies per unit mass of mtDNA. This suggests the existence of a mechanism that can compensate rather precisely for differences in mitochondrial gene dosage, perhaps by over-replication or stabilization of specific subgenomic molecules.

Mitochondrial DMA variation in somatic embryogenic cultures ofLarix

outhern hybridization analysis using wheat mitochondrial gene-specific probes indicates that changes in mitochondrial genomic organization and the relative representation of certain genomic regions occur during in vitro somatic embryogenic cell culture ofLarix species. We observed differences in the mitochondrial (mt)DNA hybridization patterns between somatic embryogenic cell cultures and trees grown from seed forLarix leptolepis,L. decidua, and the reciprocal hybrids of these twoLarix species. This is the first study to describe the correlation of molecular changes in a gymnosperm mitochondrial genome with in vitro somatic embryogenic cell culture. Quantitative differences in mtDNA hybridization signals were also observed among a 4-year-old somatic embryogenic cell culture ofLarix ×eurolepis trees regenerated from this culture, and the seed source tree from which the somatic embryogenic cell cultures were initiated.

Occurrence and transcription of genes for nad1, nad3, nad4L, and nad6, coding for NADH dehydrogenase subunits 1, 3, 4L, and 6, in liverwort mitochondria

The genes encoding subunits 1, 3, 4L, and 6 of NADH dehydrogenase (nad1, nad3, nad4L, nad6) in the mitochondrial genome of a liverwort, Marchantia polymorpha, were characterized by comparing homologies of the amino-acid sequences of the subunits with those of other organisms. The nad3 and nad4L genes are split by single and double group II introns, respectively. The 5'-half portion of the nad6 gene was repeated at an identity of 89% to form a reading frame consisting of 100 amino-acid residues. The Northern hybridization analysis showed that all four genes are transcribed in the liverwort mitochondria.

Organization of a 117-kb circular mitochondrial chromosome in IR36 rice

The organization of the mitochondrial genome in the IR36 indica variety of rice was analyzed using constant-field and CHEF gel electrophoresis. The minimum complexity of the genome is estimated to be 300 kb. There was no evidence for a master circular molecule of this size. The genome exists in vivo in multiple subgenomic circular molecules or mitochondrial chromosomes. Using several rare-cutting restriction enzymes a restriction map was constructed for a 117-kb circular chromosome. Six genetic loci have been placed on this chromosome; cox1 and atp1 have been assigned precise positions while four additional genes (rrn26, cob2, atp6 and rrn18) were mapped to restriction fragments.

Comparative analysis of a recombining-repeat-sequence family in the mitochondrial genomes of wheat (Triticum aestivum L.) and rye (Secale cereale L.)

The mitochondrial genomes of wheat and rye each contain a three-member family of recombining repeat sequences (the "18S/5S repeat") that encode genes for 18S and 5S rRNAs (rrn18 and rrn5) and tRNA(fMet) (trnfM). Here we present, for wheat and rye, the sequence and boundaries of the "common sequence unit" (CSU) that is shared between all three repeat copies in each species. The wheat CSU is 4,429 base-pairs long and contains (in addition to trnfM, rrn18 and rrn5) a putative promoter, three tRNA-like elements ("t-elements"), and part of a pseudogene ("psi atpAc") that is homologous to chloroplast atpA, which encodes the alpha subunit of chloroplast F1 ATPase. The rye CSU is somewhat smaller (2,855 base pairs) but contains much the same genic and other sequence elements as its wheat counterpart, except that two of the three t-elements as well as psi atpAc are found in only one of the three downstream flanks of the 18S/5S repeat, outside the CSU boundaries. In interpreting the sequence data in terms of the evolutionary history of the 18S/5S-repeat family of wheat and rye, we conclude that: (1) the wheat-rye form of the 18S/5S repeat most likely originated between 3 and 14 million years ago, in a lineage that gave rise to wheat and rye but not to barley, oats, rice or maize; (2) the close linkage (1-bp apart) between trnfM and rrn18 is similarly limited in its taxonomic distribution to the wheat/rye lineage; (3) the trnfM-rrn18 pair arose via a single mutation that inserted a sequence block containing trnfM immediately upstream of rrn18; and (4) the presence of a putative promoter upstream of rrn18 in all wheat and rye repeats is consistent with all three repeat copies being transcriptionally active. We discuss these conclusions in the light of the possible functional significance of recombining-repeats in plant mitochondrial genomes.