only species ( and subspecies ) for which complete mitochondrial and plastid genome sequences are available ( as of 1 march 2011 ) ( based on genbank 's entrez organelle genome database : http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome ) were included in the mtpt / ptmt analyses .
this is because organelle genomes often contain sequences ( particularly intergenic and repetitive dna ) that are species specific .
moreover , organelle gene contents can vary significantly among certain lineages , especially green algae .
mitochondrial and plastid genomes were scanned for mtpts and ptmts with blastn ( v2.2.23 ) ( altschul et al .
1990 ) using an expectation value ( e value ) of 0.0001 , a word size of 11 , match and mismatch scores of 2 and 3 , and gap - cost values of 5 ( existence ) and 2 ( extension ) .
hits under 30 nt and showing less than 70% sequence identity to the query were ignored .
spurious hits , such as those where plastid genes matched to homologous genes in the mitochondrial genome ( e.g. , plastid - encoded ribosomal dna [ rdna ] matching to mitochondrial - encoded rdna ) were ignored .
regions of mtdna that contained tight clusters of mtpts ( i.e. , ptdna - like sequences interrupted by mitochondrial sequence that did not show sequence identity to ptdna ) were counted as separate hits .
most of the ptdna - derived sequences that were identified within the mitochondrial genomes represented noncoding dna or pseudogenes ; however , instances of functional relocation of ptdna - encoded genes ( e.g. , transfer rnas ) to the mitochondrial genome were considered as mtpts .
complete mtpt statistics for the various plastid - bearing species that were investigated are shown in table 1 and figure 1 .
none of the monoplastidic or effectively monoplastidic taxa had plastid - like dna in their mitochondrial genomes , whereas all but one of the polyplastidic species contained mtpts .
the green alga chara vulgaris was the only polyplastidic species that did not have mtpts , a feature which may reflect the small number of plastids within its reproductive tissues ( 16 ) ( pickett - heaps 1975 ; renzaglia and garbary 2001 ) and its increased ability to expunge excess mtdna relative to other polyplastidic species ( discussed further below ) . on average ,
the largest numbers of mtpts were found in the mitochondrial genomes of the common grape vitis vinifera and the grass sorghum bicolor , both of which had 15 kb of plastid - derived dna , distributed among 30 different regions ( table 1 and fig .
1 ) . unlike plastid number , being mono- or polymitochondrial appeared to have no effect on the number of observed mtpts within the mitochondrial genomes ( table 1 ) .
the results presented here on mtpts are consistent with previous investigations on ptdna - like sequences in nuclear genomes ( nupts ) ( smith et al .
2011 ) , which showed that polyplastidic taxa had on average 80 times more nupts than species that were monoplastidic or effectively so .
together , the mtpt and nupt data support the hypothesis that monoplastidy greatly reduces the potential for intercompartmental ptdna migration .
bar graph showing the number and accumulative length of ptdna - derived sequences ( mtpts ) within the mitochondrial genomes of various plastid - harboring eukaryotes . for references and notes on the number of organelles per cell ,
mtpt abundance scaled exponentially with both mitochondrial genome size and mtdna noncoding content ( fig .
the most bloated mtdnas that were explored  those belonging to the angiosperms v. vinifera , s. bicolor , carica papaya , and zea mays  had the largest mtpt contents .
this relationship is not surprising given that other types of excess dna , including introns , repetitive elements , and intergenic dna , are known to mutually expand as the number of noncoding nucleotides in a mitochondrial genome increases ( lynch et al .
it is thought that the burden of harboring surplus mtdna is positively proportional to the mitochondrial mutation rate ( lynch et al .
2006 ) ; thus , the very low mtdna mutation rates that are typically found in angiosperms ( lynch et al . 2006 and references therein ) may promote the accumulation of mtpts . in this context , it is noteworthy that angiosperm mtdnas often contain nucdna - derived sequences as well as genes horizontally acquired from other mitochondrial genomes ( richardson and palmer 2007 ; kleine et al . 2009 ) , reinforcing the notion that they are sponges for all types of foreign dna . among the polyplastidic species that were investigated , the green alga c. vulgaris had the smallest and most compact mtdna ( supplementary table s1 , supplementary material online ) , implying that it is more proficient than its land plant counterparts at eliminating ( or preventing the accumulation of ) excess nucleotides from its mitochondrial genome .
if true , this may help explain why it was the only polyplastidic taxa without mtpts .
the relationship between mtpts and genome size is in accordance with previous investigations on organelle - to - nucleus dna transfers , which found that bloated nuclear genomes harbor more plastid- and mitochondrial - derived sequences than those that are compact ( hazkani - covo et al .
2011 ) . ultimately , these data suggest that the probability of transferred organelle dna persisting in a genome is largely governed by the forces controlling the expansion and contraction of bulk dna .
plot of mtpt content versus mitochondrial genome size ( log scale ) ( a ) and mitochondrial genome noncoding dna content ( b ) .
data on mitochondrial genome size and noncoding dna content are shown in supplementary table s1 ( supplementary material online ) .
not 1 of the 42 species employed here contained mtdna - like sequences in its plastid genome , irrespective of the number of mitochondria per cell and plastid genome size ( table 1 and supplementary table s1 , supplementary material online ) .
this strengthens the commonly held view that the exchange of dna between plastids and mitochondria is a one - way street ( richardson and palmer 2007 ; kleine et al .
it has been suggested that because plastid genomes are often more compact than their mitochondrial counterparts ( particularly for land plants and certain lineages of green algae ) they are more efficient than mtdnas at purging excess nucleotides .
however , this hypothesis seems unlikely when considering that no ptmts were found within the ptdna of the polymitochondrial green alga volvox carteri , which boasts a plastid genome that is larger ( > 525 kb ) and more expanded ( 80% noncoding ) than many angiosperm mtdnas ( smith and lee 2010 ) . as noted by previous investigators
( richardson and palmer 2007 ) , an intriguing observation concerning the presence of mtpts in mtdnas and the absence of ptmts from ptdnas is that mitochondria ( at least those of land plants and mammals ) have an active dna import system ( koulintchenko et al .
as predicted by the limited transfer window hypothesis , mtpts were abundant in polyplastidic species , particularly those with expanded mitochondrial genomes , and were absent from monoplastidic species as well as polyplastidic taxa with monoplastidic meristematic systems .
neither the polymitochondrial nor the monomitochondrial taxa contained mtdna - derived sequences in their plastid genomes , which may reflect the absence of an efficient dna import system within plastids .
these results , like those on plastid - like sequences in nuclear genomes , support the idea that monoplastidy limits the potential for ptdna to be donated to other organelles .
the probability that ptdna sequences will be taken up by those organelles and persist as mtpts or nupts is defined by an organelle 's ability ( or lack thereof ) to both import exogenous dna and retain it within its genome .
supplementary tables s1 and s2 are available at genome biology and evolution online ( http://www.gbe.oxfordjournals.org/ ) .
 mitochondrial genomes often contain large amounts of plastid dna ( ptdna)-derived sequences ( mtpts ) . 
 it has been suggested that the intercompartmental transfer of ptdna is greatly reduced in species with only a single plastid per cell ( monoplastidic ) as compared with those with many plastids per cell ( polyplastidic ) . 
 this hypothesis has not been applied to the movement of dna from plastids to mitochondria . by analyzing the organelle genomes from diverse mono- and polyplastidic taxa , 
 i show that mtpts are restricted to the mitochondrial genomes of species with many plastids per cell and are absent from those with one plastid per cell or with monoplastidic meristematic systems . moreover , the most bloated mitochondrial genomes that were explored had the largest mtpt contents . 
 these data , like previous results on ptdna - derived sequences in nuclear genomes , support the hypothesis that plastid number and the forces governing the expansion and contraction of noncoding mitochondrial dna ( mtdna ) influence mtpt abundance . 
 i also show that plastid genomes are depauperate in mtdna - derived sequences ( ptmts ) , irrespective of the number of mitochondria per cell and plastid genome size , which may reflect the lack of a dna uptake system in plastids . 
Materials and Methods
More Plastids, More MTPTs
More Genome, More MTPTs
Plastids Can Dish It Out but Can't Take It
Concluding Remarks
Supplementary Material