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.
Background The factors that maintain phenotypic and genetic variation within a population have received long-term attention in evolutionary biology. Here the genetic basis and evolution of the geographically widespread variation in twig trichome color (from red to white) in a shrub Melastoma normale was investigated using Pool-seq and evolutionary analyses. Results The results show that the twig trichome coloration is under selection in different light environments and that a 6-kb region containing an R2R3 MYB transcription factor gene is the major region of divergence between the extreme red and white morphs. This gene has two highly divergent groups of alleles, one of which likely originated from introgression from another species in this genus and has risen to high frequency (> 0.6) within each of the three populations under investigation. In contrast, polymorphisms in other regions of the genome show no sign of differentiation between the two morphs, suggesting that genomic patterns of diversity have been shaped by homogenizing gene flow. Population genetics analysis reveals signals of balancing selection acting on this gene, and it is suggested that spatially varying selection is the most likely mechanism of balancing selection in this case. Conclusions This study demonstrate that polymorphisms on a single transcription factor gene largely confer the twig trichome color variation in M. normale, while also explaining how adaptive divergence can occur and be maintained in the face of gene flow.
Osbeckia stellata (Melastomataceae) is a shrub distributed in the South. Although many species of Osbeckia have important medicinal value, the phylogenetic position of Osbeckia within the family Melastomataceae remains unclear. Osbeckia stellata is one of the most widespread species in this genus. Here, we reported and characterized the complete chloroplast genome sequence of O. stellata assembled from Illumina sequencing reads. The chloroplast genome size is 156,372 bp, containing a large single copy (LSC) region of 85,741 bp, a short single copy (SSC) region of 17,115 bp, and a pair of inverted repeats (IRs) of 26,758 bp. We predicted a total of 136 genes consisting of 86 protein-coding genes, 48 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that O. stellata was sister to Melastoma candidum.
Ixonanthes chinensis (Ixonanthaceae) is an endangered tree species distributed in South China and Vietnam. The phylogenetic position of Ixonanthes in the order Malpighiales remains controversial. Here we reported and characterized the complete chloroplast genome sequence of I. chinensis assembled from Illumina sequencing reads. The chloroplast genome size is 155,296 bp, containing a large single copy (LSC) region of 83,829 bp, a short single copy (SSC) region of 18,917 bp, and a pair of inverted repeats (IRs) of 26,275 bp. We predicted a total of 139 genes, which included 87 protein-coding genes, 44 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that I. chinensis was sister to Linum usitatissimum from the family Linaceae rather than Erythroxylum novogranatense from the family Erythroxylaceae.
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