Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma.

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.

Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica.

Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors. Here, however, we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica (Asphodelaceae), a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia. This structural variation, caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92-bp segment in the large single-copy region (LSC), generates a giant plastome (228 878 bp) with the largest inverted repeat of 105 226 bp and the smallest LSC of 92 bp known in land plants. It also generates an ~7-kb deletion on the boundary of the LSC, which eliminates three protein coding genes (psbA, matK, and rps16) and one tRNA gene (trnK). Albino sectors exhibit dramatic changes in expression of many plastid genes, including negligible expression of psbA, matK, and rps16, reduced expression of photosynthesis-related genes, and increased expression of genes related to the translational apparatus. Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals, and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals. These poorly developed chloroplasts likely carry the large and rearranged plastome, which is likely responsible for the loss of photosynthesis and albinism in the leaf margins. Considering that short repeats are relatively common in plant plastomes and that photosynthesis is not necessary for albino sectors, structural variation of this kind may not be rare in the plastomes of variegated plants.

The Mitochondrial Genome of the Holoparasitic Plant Thonningia sanguinea Provides Insights into the Evolution of the Multichromosomal Structure.

Multichromosomal mitochondrial genome (mitogenome) structures have repeatedly evolved in many lineages of angiosperms. However, the underlying mechanism remains unclear. The mitogenomes of three genera of Balanophoraceae, namely Lophophytum, Ombrophytum, and Rhopalocnemis, have already been sequenced and assembled, all showing a highly multichromosomal structure, albeit with different genome and chromosome sizes. It is expected that characterization of additional lineages of this family may expand the knowledge of mitogenome diversity and provide insights into the evolution of the plant mitogenome structure and size. Here, we assembled and characterized the mitogenome of Thonningia sanguinea, which, together with Balanophora, forms a clade sister to the clade comprising Lophophytum, Ombrophytum, and Rhopalocnemis. The mitogenome of T. sanguinea possesses a multichromosomal structure of 18 circular chromosomes of 8.7-19.2 kb, with a total size of 246,247 bp. There are very limited shared regions and poor chromosomal correspondence between T. sanguinea and other Balanophoraceae species, suggesting frequent rearrangements and rapid sequence turnover. Numerous medium- and small-sized repeats were identified in the T. sanguinea mitogenome; however, no repeat-mediated recombination was detected, which was verified by Illumina reads mapping and PCR experiments. Intraspecific mitogenome variations in T. sanguinea are mostly insertions and deletions, some of which can lead to degradation of perfect repeats in one or two accessions. Based on the mitogenome features of T. sanguinea, we propose a mechanism to explain the evolution of a multichromosomal mitogenome from a master circle, which involves mutation in organellar DNA replication, recombination and repair genes, decrease of recombination, and repeat degradation.

Natural hybridization between Phyllagathis and Sporoxeia species produces a hybrid without reproductive organs.

Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.

The complete chloroplast genome of Macrothelypteris torresiana, a reputed medicinal fern (Thelypteridaceae).

Macrothelypteris torresiana is a reputed medicinal fern. Its complete chloroplast genome was determined by Illumina paired-end sequencing. The genome is 151,150 bp in length with 43.1% overall Guanine+Cytosine (GC) content, which is divided into four distinct parts such as a small single copy (SSC, 21,772 bp), a large single copy (LSC, 82,422 bp), and two inverted repeats (IRs, 23,478 bp each). It contains 132 genes, including 86 protein-coding genes, eight ribosomal RNA genes, 35 tRNA genes, and three pseudogenes. Maximum likelihood (ML) tree revealed that M. torresiana was closely grouped with Christella appendiculata with 100% bootstrap value.