No abstract

Background: With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica, a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function. Results: The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial and/or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathway is partially retained, although chlorophyll synthesis is not possible. Conclusions: Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and/or mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.

Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome.

Background: With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica, a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function. Results: The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathways are partially retained, although chlorophyll synthesis is not possible.Conclusions: Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.

Shifts from cis-to trans-splicing of mitochondrial introns tend to correlate with relative genome rearrangement rates during vascular plant evolution, as is particularly apparent in some lineages of gymnosperms. However, although many angiosperms have also relatively high mitogenomic rearrangement rates, very few cis-to trans-splicing shifts except for five trans-spliced introns shared in seed plants have been reported. In this study, we sequenced and characterized the mitogenome of Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). The mitogenome was assembled into a circular chromosome of 256,961 bp long, relatively small compared with its relatives from Santalales. It possessed a gene content of typical angiosperm mitogenomes, including 33 protein-coding genes, three rRNA genes and ten tRNA genes. Plastid-derived DNA fragments took up 9.1% of the mitogenome. The mitogenome contained one group I intron (cox1i729) and 23 group II introns. We found shifts from cis-to trans-splicing of five additional introns in its mitogenome, of which two are specific in T. maclurei. Moreover, atp1 is a chimeric gene and phylogenetic analysis indicated that a 356 bp region near the 3′ end of atp1 of T. maclurei was acquired from Lamiales via horizontal gene transfer. Our results suggest that shifts to trans-splicing of mitochondrial introns may not be uncommon among angiosperms.

The mangrove fern Acrostichum aureum is widely distributed in the Indo West-Pacific and Atlantic East-Pacific regions. Here we assembled and annotated its chloroplast genome based on the Illumina sequencing reads. The complete chloroplast genome of A. aureum was 154,805 bp in length with the GC content of 38.38%. It contains a large single copy (LSC) region of 82,826 bp and a small single copy (SSC) region of 21,617 bp, separated by a pair of inverted repeat region (IRs) of 25,181 bp each. It contains 84 protein coding genes, 27 tRNA genes, and four rRNA genes. Phylogenetic analysis shows that A. aureum is closest to Ceratopteris cornuta in the subfamily Parkerioideae. The chloroplast genome of A. aureum reported here offers a useful resource for its phylogeography and conservation genetics studies.

The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50–99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genome, and approximately 50% of repeats (< 350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373 and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.

Background Mitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized. Results Here we assembled and characterized the mitogenomes of three species of Melastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes of M. candidum (Mc), M. sanguineum (Ms) and M. dodecandrum (Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species, M. penicillatum, which has not been fixed as it is only found in one of the three examined populations. Conclusions By characterizing mitochondrial genome sequences of Melastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species.