BACKGROUND
the obvious expansion of its genomic size indicates that higher plant mitochondria experienced a dramatic evolution.
the common size of mitochondria genetic information is limited to approximately  <dig> kb in metazoans  <cit> , whereas in higher plants the sequence length can be 200- <dig> kb   <cit> .
the principal role of mitochondria  is undoubtedly shared between metazoans and higher plants.
the presence of three genes encoding subunits of atp synthase , three genes encoding subunits of cytochrome oxidase , cytochrome b , and seven genes for nadh dehydrogenase  is indeed conserved in mitochondria of both kingdoms.
what is extra in plant mitochondria compared to that of metazoans are only a few more respiratory-related genes  and dozens of genes encoding ribosomal subunits .
thus, usually a higher plant mitochondrion encodes about  <dig> genes with known functions, whereas in most cases there are  <dig> tightly conserved genes encoded by metazoan mitochondria.
thus, a greater number of mitochondrial genes would explain only a small proportion of the genome size increase of plant mitochondria.
a partial answer to the mysterious expansion of mitochondrial genome size was given by recent plant mitochondrial genome sequencing studies.
according to ncbi , mitochondrial genome sequencing of  <dig> magnolyophyta species is currently complete.
these include dicot species arabidopsis thaliana  <cit> , beta vulgaris  <cit> , brassica napus  <cit>  and nicotiana tabacum  <cit> ; and monocots oryza sativa  <cit> , zea mays  <cit>  and triticum aestivum  <cit> .
these studies not only reported the great variability in size and gene content of mitochondria among species, but also even within species mitochondrial genomic structure can vary significantly.
for example, different z. mays lineages can carry mitochondrial genomic information of range 536- <dig> kb  <cit> .
much of the size differences of these genomes are due to different numbers of large genomic duplication events, and apparent genomic recombination events between lineages.
the comparison of a b. vulgaris cytoplasmic male sterile  strain with the non-cms strain showed a complex rearrangement of sequence blocks  <cit> .
we recently sequenced two cms strains of rice , and at least  <dig> genomic recombination events were necessary to explain the origin of the mitochondrial genome compared to the reference genome  <cit> .
to understand the nature of large inter-genic region, we used a 60-mer probe-tiling array to visualize the expression pattern of the entire rice mitochondrial genome.
in calli,  <dig> % of the regions could be regarded as being transcribed.
by setting the transcriptional borders by defining transcriptional units, we showed that  <dig> % of open reading frames  present in inter-genic regions were being transcribed without association with known mitochondrial housekeeping genes.
we also identified two different partial fragments of transposable elements  that were being transcribed, suggesting unexpected complexity of transcriptional regulation in plant mitochondria.
RESULTS
experimental design
the mitochondrial genome size of nipponbare, the rice cultivar commonly used in molecular biology, is estimated at  <dig>  <dig> bp  <cit> .
tiling probes of  <dig> mer were designed for  <dig> 866-bp non-redundant sequences after discarding large duplicated regions of >  <dig>  <dig> bp.
the probes overlapped each other by  <dig> nucleotides, meaning that tiling probes with 2-bp intervals were designed for the  <dig> 866-bp region.
mitochondrial rna was prepared from calli or etiolated-seedlings and hybridized against the tiling probes after biotin labeling upon reverse transcription by random primers.
for further information on the processing of tiling array output, such as expression value normalization, see methods.
identification of transcribed region
to restrict the transcribed region, we used the relative transcription levels of orf <dig> and orf <dig> as background  controls.
transcripts of these two orfs were not detected in our preliminary transcription analysis by northern blotting .
these genes are partly te fragments, making them highly unlikely to have any function in mitochondria, and therefore we concluded that these genes were not transcribed.
a sliding window was set as a cluster of  <dig> consecutive probes, and normalized expression values of each sliding window were compared against  <dig> probes spanning the regions of orf <dig> and orf <dig>  if the mean value of each window significantly exceeded the mean value of the  <dig> probes , the window was considered to represent an expressed region.
as a result, we estimated that  <dig> % of the mitochondrial genome was being transcribed in rice calli, compared to only  <dig> % in etiolated seedlings.
the discrepancy between these values is mostly explained by being a region without annotations of previously known mitochondrial housekeeping genes.
for simplicity we designated the region without previous annotations by known mitochondrial genes the 'inter-genic' regions.
positive correlations of rna expression between the two tissues  were higher in the previously annotated housekeeping genes  than in the orfs predicted by six-frame translation in inter-genic regions  .
this indicates that rna expression regulation of known housekeeping gene models was well conserved between the two tissues, while expression of the inter-genic region was less conserved.
all regions carrying known mitochondrial genes were regarded as being transcribed under the above statistics we used .
almost all probes within the known genic regions gave p <  <dig> , thus, the criterion we used to choose the expressed region was correct at least in this sense.
transcriptional units in inter-genic regions
to comprehensively reveal the rna expressional regulation of inter-genic regions, it was necessary to make a clear distinction between transcripts that were associated with known housekeeping genes , and the transcripts that were not associated with these gene features.
therefore, we designated each continuously expressed region  as a 'transcriptional unit' .
this region contained a highly expressed  <dig> s ribosomal rna gene , and there was a high chance of rna expression in this region , and of high scores for relative rna expression level.
these consecutive low p-value regions with a 'valley'-like transcriptional landscape were termed as single tus in this study for brevity.
although there were relatively lower chances of rna expression, this region contained four more tus  other than the rrn <dig> tu.
further details of tus are described in the materials and methods.
as a result of tu searches using the p <  <dig>  criterion, we detected  <dig> and  <dig> tus in calli and seedlings, respectively.
all tus detected in seedlings were also identified in calli, suggesting that rna regulation of calli was far more complex, or otherwise leaky, compared to that of seedlings.
to determine the meanings of tus detected in inter-genic regions, we used six-frame translation to predict orfs present within these tus.
six-frame translation analysis predicted  <dig> orfs in the rice mitochondrial genome and of these,  <dig> were not annotated as mitochondrial genes .
we designated the orfs in inter-genic regions as inter-genic orfs .
these  <dig> iorfs were numbered iorf_ <dig> to iorf_ <dig>  skipping the numbers of frames corresponding to known genes  .
it should be noted that  <dig> orfs were previously designated  <cit> , but we will use our ids throughout for brevity.
among these  <dig> iorfs,  <dig> were within one of the tus that were not associated with housekeeping genes.
thus, of  <dig> tus located in the inter-genic regions,  <dig> carried at least one protein frame longer than  <dig> amino acids .
if the protein functions of these newly identified iorfs are important to mitochondrial function, we hypothesized that the extent of conservation of these orfs among the species would be positively linked with their transcription.
the idea is supported by the fact that conserved genes are generally highly expressed, whereas species-specific genes are expressed at low levels in specific tissue types  <cit> .
thus, to further understand the nature of these iorfs, we conducted a comprehensive database analysis.
using a bi-directional blast search, we sought for orthologous orfs from the exact same six-frame translation protein libraries of mitochondrial genomes of  <dig> other land plant species.
although orthologous protein frames were found from these species, there was no statistically significant correlation between frame conservation and transcript expression.
however, there were eight orfs  conserved among several species, especially among monocotyledons, and were transcribed in single tus without associating other known gene features.
an example of such orfs was iorf_ <dig>  and the presence of this frame was shared among four other monocotyledon species: sorghum bicolor, triticum aestivum, tripsacum dactyloides and z. mays.
as frames adjacent to iorf_ <dig>  were not present in these species, it was unlikely that iorf_ <dig> was conserved among species as a side effect by synteny of large genomic fragments.
thus, we presume that iorf_ <dig> may be a gene at least in monocotyledons and could possess a role in mitochondria.
we confirmed the expression of these eight iorfs by rt-pcr analysis .
this proves that signal detection of these regions was not the result of cross-hybridization.
of the eight orfs just mentioned, iorf_ <dig> and iorf_ <dig> shared similarities with tes.
according to notsu et al.
<cit> ,  <dig> tes  are present in the rice mitochondrial genome.
iorf_ <dig> had significant similarity with a part of a. thaliana retroelement polymerase polyprotein , and was previously identified  <cit> .
iorf_ <dig> had a significant similarity with part of another long terminal repeat  retrotransposon in bamboo  , and this frame was newly identified in the present study.
these two fragments of tes, iorf_ <dig> and iorf <dig>  were the only ones being transcribed among  <dig> partial tes identified in total .
although these fragments were clearly transcribed, it was unlikely that these fragments were actively transposable, given that they carry only partial sequences of a retrotransposon.
non-autonomous transposing activity was equally unlikely, as ltrs were not present in these iorfs.
discussion
in this study we conducted a rice mitochondrial genomic-tiling array to reveal the hidden factors that expanded plant mitochondrial genomic information size.
depending on the tissue type, at most  <dig> % of the mitochondrial genome was being transcribed.
transcription frequencies of iorfs can be dependent on tissue types .
several iorfs could be considered as transcribed not by coincidence, suggesting the hidden role of mitochondria.
there are currently no further hints for functions of these iorf features conserved among species.
this is because no similar protein motif was identified from non-redundant protein database searches, and it is not easy to speculate their protein function even if they were translated.
alternatively, there could be a possibility that these transcripts do not encode a protein.
they could be transcribed as non-coding rna  genes.
this is supported by the fact that there are a few transcripts that do not carry orf longer than  <dig> amino acids .
for example, ncrna <dig> does not carry a reading frame longer than  <dig> codons.
it is more convincing to consider that these transcripts are ncrnas rather than to consider that they encode a protein.
to date, no ncrna-mediated gene regulation mechanism has been described in plant mitochondria.
it is possible that these inter-genic transcribed regions serving the ncrna are required for regulation of other genic regions.
one of the most important findings in the present study was the detection of transcription of two partial tes.
te fragments have been found in all plant mitochondrial genomes sequenced so far  <cit> ; however, most of them were not considered functional, as they were present only in fragments.
one possibility is the detection of contaminated nuclear rna.
however, nucleotide identities of these two tes  with their respective nuclear sister copies were  <dig>  and  <dig> %, low enough to be washed off during the post-hybridization processing.
secondly, transcript detection of te fragments from nuclear rna contamination seems odd, when considering that there were  <dig> te-like sequences present in mitochondria and that transcripts for  <dig> were not detected, even though they too possess decent numbers of nuclear sister copies.
we have also confirmed the rna expression of iorf_ <dig> and iorf_ <dig> by rt-pcr analysis .
lastly, as unrestricted transposition of tes may cause deleterious genomic mutations, the majority of nuclear tes would be suppressed by dna methylation  <cit> .
indeed, best sister copies of each mitochondrial te fragment were not transcribed, according to the nuclear tiling array profile in the tigr rice genome browser  <cit> .
therefore we consider that false-detection of a nuclear copy was unlikely in this case.
although these te fragments  are unlikely to possess transposing activities given the incomplete fragments of te protein sequences they carry , it is likely that they are the remnants of past te integration into the mitochondrial genome.
recent study of rna editing site loss in silene spp.
has shown evidence of integration of reverse-transcribed mrna into mitochondrial genome  <cit> .
it is possible that similar re-integration events can occur for other mitochondrial rna.
in the present study we showed that the mitochondrial rna pool is a mixture of various transcripts from unexpected places within the genome.
re-integration of such transcripts might have contributed to complexity of flowering plant mitochondria compared to other species.
a good example is the chimeric structure of most cms-related genes, which are often present as the fused chimeric protein of partial respiratory chain subunit and an unknown sequence  <cit> .
the peptide region of an unknown sequence can originate from inter-genic transcripts; these sequences may be quickly lost during evolution and missing in extant species, while they can be retained as a part of cms-related gene.
this might be one explanation for why sequences of unknown origin are often found within cms-related genes.
approximately 50% of a typical plant mitochondrial genome does not show any similarities with other plant mitochondrial genomes  <cit> , suggesting the involvement of frequent genomic recombination or horizontal transfer events in enlargement of the plant mitochondrial genome.
it is also possible that as mitochondria alter their genomic arrangement quite frequently  <cit> , nuclear-encoded rna polymerases are not yet adapted to optimize the transcriptional efficiency of mitochondria.
this could be the reason why so many inter-genic regions that are seemingly unrelated to mitochondrial functions are being transcribed by residual functions of un-optimized rna polymerases.
CONCLUSIONS
we conclude that the plant mitochondrion is enriched with unknown transcripts that are mapped on inter-genic regions.
this is obviously related to the large genomic information size of plant mitochondria, and revealing the functions of these transcripts should improve our understanding of the expansion of the plant mitochondrial genome.
finally, the results presented here are publicly accessible as oryza sativa mitochondrial rna expression server .

 the obvious expansion of its genomic size indicates that higher plant mitochondria experienced a dramatic evolution. the common size of mitochondria genetic information is limited to approximately kb in metazoans, whereas in higher plants the sequence length can be 200- kb. the principal role of mitochondria is undoubtedly shared between metazoans and higher plants. the presence of three genes encoding subunits of atp synthase, three genes encoding subunits of cytochrome oxidase, cytochrome b, and seven genes for nadh dehydrogenase is indeed conserved in mitochondria of both kingdoms. what is extra in plant mitochondria compared to that of metazoans are only a few more respiratory-related genes and dozens of genes encoding ribosomal subunits. thus, usually a higher plant mitochondrion encodes about genes with known functions, whereas in most cases there are tightly conserved genes encoded by metazoan mitochondria. thus, a greater number of mitochondrial genes would explain only a small proportion of the genome size increase of plant mitochondria. a partial answer to the mysterious expansion of mitochondrial genome size was given by recent plant mitochondrial genome sequencing studies. according to ncbi, mitochondrial genome sequencing of magnolyophyta species is currently complete. these include dicot species arabidopsis thaliana, beta vulgaris, brassica napus and nicotiana tabacum; and monocots oryza sativa, zea mays and triticum aestivum. these studies not only reported the great variability in size and gene content of mitochondria among species, but also even within species mitochondrial genomic structure can vary significantly. for example, different z. mays lineages can carry mitochondrial genomic information of range 536- kb. much of the size differences of these genomes are due to different numbers of large genomic duplication events, and apparent genomic recombination events between lineages. the comparison of a b. vulgaris cytoplasmic male sterile strain with the non-cms strain showed a complex rearrangement of sequence blocks. we recently sequenced two cms strains of rice, and at least genomic recombination events were necessary to explain the origin of the mitochondrial genome compared to the reference genome. to understand the nature of large inter-genic region, we used a 60-mer probe-tiling array to visualize the expression pattern of the entire rice mitochondrial genome. in calli, % of the regions could be regarded as being transcribed. by setting the transcriptional borders by defining transcriptional units, we showed that % of open reading frames present in inter-genic regions were being transcribed without association with known mitochondrial housekeeping genes. we also identified two different partial fragments of transposable elements that were being transcribed, suggesting unexpected complexity of transcriptional regulation in plant mitochondria.  experimental design the mitochondrial genome size of nipponbare, the rice cultivar commonly used in molecular biology, is estimated at bp. tiling probes of mer were designed for 866-bp non-redundant sequences after discarding large duplicated regions of > bp. the probes overlapped each other by nucleotides, meaning that tiling probes with 2-bp intervals were designed for the 866-bp region. mitochondrial rna was prepared from calli or etiolated-seedlings and hybridized against the tiling probes after biotin labeling upon reverse transcription by random primers. for further information on the processing of tiling array output, such as expression value normalization, see methods. identification of transcribed region to restrict the transcribed region, we used the relative transcription levels of orf and orf as background controls. transcripts of these two orfs were not detected in our preliminary transcription analysis by northern blotting. these genes are partly te fragments, making them highly unlikely to have any function in mitochondria, and therefore we concluded that these genes were not transcribed. a sliding window was set as a cluster of consecutive probes, and normalized expression values of each sliding window were compared against probes spanning the regions of orf and orf if the mean value of each window significantly exceeded the mean value of the probes, the window was considered to represent an expressed region. as a result, we estimated that % of the mitochondrial genome was being transcribed in rice calli, compared to only % in etiolated seedlings. the discrepancy between these values is mostly explained by being a region without annotations of previously known mitochondrial housekeeping genes. for simplicity we designated the region without previous annotations by known mitochondrial genes the'inter-genic' regions. positive correlations of rna expression between the two tissues were higher in the previously annotated housekeeping genes than in the orfs predicted by six-frame translation in inter-genic regions. this indicates that rna expression regulation of known housekeeping gene models was well conserved between the two tissues, while expression of the inter-genic region was less conserved. all regions carrying known mitochondrial genes were regarded as being transcribed under the above statistics we used. almost all probes within the known genic regions gave p <, thus, the criterion we used to choose the expressed region was correct at least in this sense. transcriptional units in inter-genic regions to comprehensively reveal the rna expressional regulation of inter-genic regions, it was necessary to make a clear distinction between transcripts that were associated with known housekeeping genes, and the transcripts that were not associated with these gene features. therefore, we designated each continuously expressed region as a'transcriptional unit'. this region contained a highly expressed s ribosomal rna gene, and there was a high chance of rna expression in this region, and of high scores for relative rna expression level. these consecutive low p-value regions with a'valley'-like transcriptional landscape were termed as single tus in this study for brevity. although there were relatively lower chances of rna expression, this region contained four more tus other than the rrn tu. further details of tus are described in the materials and methods. as a result of tu searches using the p < criterion, we detected and tus in calli and seedlings, respectively. all tus detected in seedlings were also identified in calli, suggesting that rna regulation of calli was far more complex, or otherwise leaky, compared to that of seedlings. to determine the meanings of tus detected in inter-genic regions, we used six-frame translation to predict orfs present within these tus. six-frame translation analysis predicted orfs in the rice mitochondrial genome and of these, were not annotated as mitochondrial genes. we designated the orfs in inter-genic regions as inter-genic orfs. these iorfs were numbered iorf_ to iorf_ skipping the numbers of frames corresponding to known genes. it should be noted that orfs were previously designated, but we will use our ids throughout for brevity. among these iorfs, were within one of the tus that were not associated with housekeeping genes. thus, of tus located in the inter-genic regions, carried at least one protein frame longer than amino acids. if the protein functions of these newly identified iorfs are important to mitochondrial function, we hypothesized that the extent of conservation of these orfs among the species would be positively linked with their transcription. the idea is supported by the fact that conserved genes are generally highly expressed, whereas species-specific genes are expressed at low levels in specific tissue types. thus, to further understand the nature of these iorfs, we conducted a comprehensive database analysis. using a bi-directional blast search, we sought for orthologous orfs from the exact same six-frame translation protein libraries of mitochondrial genomes of other land plant species. although orthologous protein frames were found from these species, there was no statistically significant correlation between frame conservation and transcript expression. however, there were eight orfs conserved among several species, especially among monocotyledons, and were transcribed in single tus without associating other known gene features. an example of such orfs was iorf_ and the presence of this frame was shared among four other monocotyledon species: sorghum bicolor, triticum aestivum, tripsacum dactyloides and z. mays. as frames adjacent to iorf_ were not present in these species, it was unlikely that iorf_ was conserved among species as a side effect by synteny of large genomic fragments. thus, we presume that iorf_ may be a gene at least in monocotyledons and could possess a role in mitochondria. we confirmed the expression of these eight iorfs by rt-pcr analysis. this proves that signal detection of these regions was not the result of cross-hybridization. of the eight orfs just mentioned, iorf_ and iorf_ shared similarities with tes. according to notsu et al., tes are present in the rice mitochondrial genome. iorf_ had significant similarity with a part of a. thaliana retroelement polymerase polyprotein, and was previously identified. iorf_ had a significant similarity with part of another long terminal repeat retrotransposon in bamboo, and this frame was newly identified in the present study. these two fragments of tes, iorf_ and iorf were the only ones being transcribed among partial tes identified in total. although these fragments were clearly transcribed, it was unlikely that these fragments were actively transposable, given that they carry only partial sequences of a retrotransposon. non-autonomous transposing activity was equally unlikely, as ltrs were not present in these iorfs. discussion in this study we conducted a rice mitochondrial genomic-tiling array to reveal the hidden factors that expanded plant mitochondrial genomic information size. depending on the tissue type, at most % of the mitochondrial genome was being transcribed. transcription frequencies of iorfs can be dependent on tissue types. several iorfs could be considered as transcribed not by coincidence, suggesting the hidden role of mitochondria. there are currently no further hints for functions of these iorf features conserved among species. this is because no similar protein motif was identified from non-redundant protein database searches, and it is not easy to speculate their protein function even if they were translated. alternatively, there could be a possibility that these transcripts do not encode a protein. they could be transcribed as non-coding rna genes. this is supported by the fact that there are a few transcripts that do not carry orf longer than amino acids. for example, ncrna does not carry a reading frame longer than codons. it is more convincing to consider that these transcripts are ncrnas rather than to consider that they encode a protein. to date, no ncrna-mediated gene regulation mechanism has been described in plant mitochondria. it is possible that these inter-genic transcribed regions serving the ncrna are required for regulation of other genic regions. one of the most important findings in the present study was the detection of transcription of two partial tes. te fragments have been found in all plant mitochondrial genomes sequenced so far; however, most of them were not considered functional, as they were present only in fragments. one possibility is the detection of contaminated nuclear rna. however, nucleotide identities of these two tes with their respective nuclear sister copies were and %, low enough to be washed off during the post-hybridization processing. secondly, transcript detection of te fragments from nuclear rna contamination seems odd, when considering that there were te-like sequences present in mitochondria and that transcripts for were not detected, even though they too possess decent numbers of nuclear sister copies. we have also confirmed the rna expression of iorf_ and iorf_ by rt-pcr analysis. lastly, as unrestricted transposition of tes may cause deleterious genomic mutations, the majority of nuclear tes would be suppressed by dna methylation. indeed, best sister copies of each mitochondrial te fragment were not transcribed, according to the nuclear tiling array profile in the tigr rice genome browser. therefore we consider that false-detection of a nuclear copy was unlikely in this case. although these te fragments are unlikely to possess transposing activities given the incomplete fragments of te protein sequences they carry, it is likely that they are the remnants of past te integration into the mitochondrial genome. recent study of rna editing site loss in silene spp. has shown evidence of integration of reverse-transcribed mrna into mitochondrial genome. it is possible that similar re-integration events can occur for other mitochondrial rna. in the present study we showed that the mitochondrial rna pool is a mixture of various transcripts from unexpected places within the genome. re-integration of such transcripts might have contributed to complexity of flowering plant mitochondria compared to other species. a good example is the chimeric structure of most cms-related genes, which are often present as the fused chimeric protein of partial respiratory chain subunit and an unknown sequence. the peptide region of an unknown sequence can originate from inter-genic transcripts; these sequences may be quickly lost during evolution and missing in extant species, while they can be retained as a part of cms-related gene. this might be one explanation for why sequences of unknown origin are often found within cms-related genes. approximately 50% of a typical plant mitochondrial genome does not show any similarities with other plant mitochondrial genomes, suggesting the involvement of frequent genomic recombination or horizontal transfer events in enlargement of the plant mitochondrial genome. it is also possible that as mitochondria alter their genomic arrangement quite frequently, nuclear-encoded rna polymerases are not yet adapted to optimize the transcriptional efficiency of mitochondria. this could be the reason why so many inter-genic regions that are seemingly unrelated to mitochondrial functions are being transcribed by residual functions of un-optimized rna polymerases.  we conclude that the plant mitochondrion is enriched with unknown transcripts that are mapped on inter-genic regions. this is obviously related to the large genomic information size of plant mitochondria, and revealing the functions of these transcripts should improve our understanding of the expansion of the plant mitochondrial genome. finally, the results presented here are publicly accessible as oryza sativa mitochondrial rna expression server. 
plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. the present study indicated the previously unexpected complexity of plant mitochondrial rna metabolism. whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of rna expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. the newly identified open reading frames predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these orfs did not play a role in mitochondrial principal functions.
 plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. we used a genomic tiling array to draw a transcriptomic atlas of oryza sativa japonica mitochondria, which was predicted to be approximately 490-kb long.  whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of rna expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. the newly identified open reading frames predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these orfs did not play a role in mitochondrial principal functions. we also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria.  the present study indicated the previously unexpected complexity of plant mitochondrial rna metabolism. our transcriptomic data is publicly accessible at. 