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Hildenbrandia is an early diverged lineage in Florideophyceae, Rhodophyta. The species diversity of this genus is still unresolved due to the simple morphology and limited molecular information. The mitochondrial genome of freshwater H. jigongshanensis was determined in this study. The freshwater H. jigongshanensis had a larger mitochondrial genome than the marine H. rubra and GC content was higher. Collinear alignment structure was observed between the mitochondrial genomes of H. jigongshanensis and H. rubra, except for one block that was encoded on the complement strand. More introns were found in mitochondrial genome of H. jigongshanensis than in H. rubra, and H. jigongshanensis shares the common feature with Bangiophyceae that two introns were distributed in cox1. Comparison of mitochondrial genome organization suggests that H. jigongshanensis preserves characters that could be hypothetically more similar to the ancestor of Bangiophyceae and Florideophyceae, which differ with previous studies based on chloroplast, and nuclear markers. More mitochondrial genomes and phylogenetic analyses combing nuclear, chloroplast and mitochondrial genomes are needed to clarify this discrepancy. Mitochondrion-based phylogeny in this study resulted in better solution at both the deep and recent derived nodes than single-gene phylogenies. Most protein-coding genes between H. jigongshanensis and H. rubra were identical except atp8, which was present in H. jigongshanensis while absent from H. rubra. This finding follows the trend that high Ka/Ks ratio genes are more frequently lost than low Ka/Ks ratio ones in red algae. [ABSTRACT FROM AUTHOR]

Main conclusion: The first complete mitochondrial genome of Carex (C. breviculmis) was sequenced and assembled, and its genomic signature was analyzed and the possible conformations of its mitochondrial genome were validated. Carex breviculmis is a very adaptable grass that is highly resistant to environmental stresses such as drought and low light. It is also admired as a landscape plant with high development prospects and scientific research value. In this study, the mitochondrial genome of C. breviculmis was assembled using Pacbio and Illumina sequencing data. We detected 267 pairs of repeats and found that three pairs of repeats could mediate the recombination of its mitochondrial genome and formed four possible conformations, of which we verified the two conformations mediated by the shortest pair of repeats using PCR amplification and Sanger sequencing. The major conformation of the C. breviculmis mitochondrial genome is a 1,414,795 bp long circular molecule with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected a total of 25 homologous sequences between the chloroplast and mitochondrial genomes, corresponding to 0.40% of the mitochondrial genome. Combined with the low GC content (41.24%), we conclude that the reduction in RNA editing sites in the C. breviculmis mitochondrial genome may be due to an accumulation of point mutations in C-to-T or retroprocessing events within the genome. The relatively low number of RNA editing sites in its mitochondrial genome could serve as important material for subsequent studies on the selection pressure of RNA editing in angiosperms. A maximum likelihood analysis based on 23 conserved mitochondrial genes from 28 species reflects an accurate evolutionary and taxonomic position of C. breviculmis. This research provided us with a comprehensive understanding of the mitochondrial genome of Carex and also provided important information for its molecular breeding. [ABSTRACT FROM AUTHOR]

The reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species' taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species' native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored. [ABSTRACT FROM AUTHOR]

The plastid gene psbD encodes D2, a photosystem II reaction center chlorophyll-binding protein. psbD is transcribed from a conserved chloroplast promoter that is activated by blue, white, or UV-A light. In this study, various forms of the barley ( Hordeum vulgare L.) chloroplast psbD-LRP were fused to the uidA reporter gene and introduced into the tobacco ( Nicotiana tabacum L.) plastid genome through homologous recombination. Primer extension analysis of transcripts from the psbD-LRP- uidA construct showed that the barley psbD-LRP was activated in tobacco by blue or white light. Transcription from this construct was also regulated by circadian cycling indicating that the barley psbD-LRP could respond to light modulated regulatory pathways in tobacco. Mutation of the psbD-LRP prokaryotic −10 promoter element reduced transcription to very low levels in all light regimes. In contrast, mutation of a prokaryotic −35 promoter element had no effect on transcription from the psbD-LRP. Deletion or mutation of an upstream activating element, the AAG-box (−36 to −64), also reduced transcription from the construct to very low levels. In contrast, deletion of the upstream PGT-box (−71 to −100) did not alter promoter activation by blue light, or responsiveness to circadian cycling. These in vivo studies confirm the importance of the psbD-LRP −10 promoter element and AAG-box in light regulation and demonstrate that these elements are sufficient to mediate circadian cycling of the barley psbD promoter. [ABSTRACT FROM AUTHOR]

Seven major plastid protein encoding genes were positioned on the soybean chloroplast DNA by heterologous hybridization. These include the genes for the alpha, beta and epsilon subunits of the CF component of ATP synthase (atpA, atpB and atpE respectively), for subunit III of the CF component of ATP synthase (atpH), for the cytochrome f (cytF), for the '32 Kd' thylakoid protein (psbA), and for the large subunit of ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcL), all of which map in the large single copy region. The atpB, atpE and rbcL genes are located in the region adjacent to one of the segments of the inverted repeat. The genetic organization of the soybean chloroplast DNA is compared to that of other plastid genomes. [ABSTRACT FROM AUTHOR]

Somatic hybrid plants have been regenerated following polyethylene glycol mediated fusion of leaf mesophyll protoplasts from tomato and protoplasts from Lycopersicon pennellii callus. Three different cultivars of tomato were used as sources of protoplasts: Early Girl, Manapal, and UC82B. Fusions were performed between protoplasts of these tomato cultivars and protoplasts of L. pennellii, and between protoplasts of the cultivars and protoplasts of L. pennellii that had been exposed to 3 or 6 krads of gamma radiation. Somatic hybrid plants were identified on the basis of heterozygous isozyme banding patterns, and leaf and flower morphology. Somatic hybrid plants were regenerated following fusion of tomato protoplasts with either untreated or irradiated L. pennellii protoplasts. All were heterozygous for isozyme loci on five different chromosomes. Regenerated somatic hybrids showed inheritance of either or both parental chloroplast genomes, but predominantly the L. pennellii mitochondrial genome. The regenerated somatic hybrid plants exhibited reduced fertility, less than 20% viable pollen. A total of 34 somatic hybrid calli were identified. Of these, 21 regenerated shoots, and 7 produced seed following manual pollinations. [ABSTRACT FROM AUTHOR]

A single somatic hybrid callus clone was identified following the fusion of Lycopersicon esculentum protoplasts and Solanum rickii suspension culture protoplasts. The hybrid nature of the callus and the plants regenerating from it was determined by assaying phosphoglucomutase-2 isozyme expression. The chloroplast genome present in four somatic hybrid plants was characterized by probing digests of total DNA with nick translated L. esculentum chloroplast DNA(cpDNA). All four somatic hybrid plants had inherited S. rickii cpDNA. Two clones of plant mitochondrial DNA (mtDNA), soybean 18S and 5S rDNA and maize cytochrome oxidase subunit II were used to characterize the mtDNA present in total DNA digests of four somatic hybrid plants. In both cases, the somatic hybrid plants had inherited most but not all of the S. rickii specific fragments, but none of the L. esculentum specific fragments. [ABSTRACT FROM AUTHOR]

Selection and screening methods were devised which resulted in the identification of a number of somatic hybrid callus clones following fusion of Lycopersicon esculentum protoplasts and L. pennellii suspension culture protoplasts. Visual selection for callus morphology combined with a high fusion frequency and irradiation of one parental protoplast type (Cs source, 1.5 Krads) resulted in selection of a callus clone population containing a high proportion of somatic hybrids. Analysis of a dimeric isozyme for the presence of a heterodimeric form was found to be satisfactory for distinguishing parental-type calli, somatic hybrid calli, and mixed calli derived from both types of unfused parental cells. No somatic hybrid calli produced shoots, although the sexual hybrid between L. esculentum and L. pennellii regenerated well under the culture conditions employed. This result suggests that the non-regenerable growth habit of the L. pennellii suspension culture was dominant in the somatic hybrid. The culture conditions described here are suitable for obtaining regenerated plants from L. esculentum mesophyll protoplasts. L. esculentum protoplast calli from fusion cultures gave rise to shoots with L. esculentum phenotype at higher frequency than calli from control unfused L. esculentum mesophyll protoplast cultures. The use of probes for species-specific organelle DNA fragments allowed identification of organelle DNA restriction fragments in digests of total DNA from small samples of individual callus clones. The callus clones analyzed either carried predominantly one parental plastid DNA type or mixtures of both types. Use of a mitochondrial DNA (mtDNA) probe which distinguishes two parental mtDNA fragments revealed that the L. pennellii-specific fragment was present in all clones examined, but the L. esculentum fragment was absent or in low proportion. [ABSTRACT FROM AUTHOR]