Maximum likelihood phylogeny of the representative rosids lineages.

<p>The common grape vine (<i>Vitis vinifera</i>) is included as the outgroup to root the tree. The concatenated alignment includes 62 conserved chloroplast genome genes and 54,689 aligned nucleotide sites. Nodes received <70% bootstrap support are indicated by gray arrows. The putative events of gene losses are inferred based on the most parsimonious scenario.</p

Chloroplast genome map of <i>Citrus aurantiifolia</i>.

<p>Gene drawn inside the circle are transcribed clockwise, whereas those outside are counterclockwise. The within-genome GC content variation is indicated in the middle circles.</p

List of long repeat sequences.

a<p>D: direct repeat; P: palindrome inverted repeat.</p>b<p>IGS: intergenic spacer region. Sequences conserved in the <i>C. sinensis</i> chloroplast genome are highlighted in bold.</p><p>List of long repeat sequences.</p

Differences between the <i>C. aurantiifolia</i> and <i>C. sinensis</i> cp genomes.

a<p>Relative to the length of <i>C. aurantiifolia.</i></p>b<p>Length in C. aurantiifolia.</p><p>Differences between the <i>C. aurantiifolia</i> and <i>C. sinensis</i> cp genomes.</p

Data_Sheet_1.DOCX

<p>Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species—Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation. To further examine whether both organelle genomes have the same manner of inheritance in other Deparia ferns, we sequenced both plastid and mitochondrial DNA regions of inter-species hybrids, and performed phylogenetic analyses to identify the origins of organellar DNA. Evidence from our experiments and phylogenetic analyses support that both organelle genomes in Deparia are uniparentally and maternally inherited. Most importantly, our study provides the first report of mitogenome inheritance in eupolypod ferns, and the second one among all ferns.</p