Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species.

We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1-99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values. Four genes, petN, psaJ, psbF, and psbN, related to photosynthesis and one gene, rpl23, related to the ribosomal large subunit remain conserved in all 10 Araliaceae species. Phylogenetic analysis revealed that the ten species could be resolved into two monophyletic lineages, the Panax-Aralia and the Eleutherococcus-Dendropanax groups, which diverged approximately 8.81-10.59 million years ago (MYA). The Panax genus divided into two groups, with diploid species including P. notoginseng, P. vietnamensis, and P. japonicus surviving in Southern Asia and a tetraploid group including P. ginseng and P. quinquefolius Northern Asia and North America 2.89-3.20 MYA.

Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays.

The imprinted Snurf-Snrpn domain, also referred to as the Prader-Willi syndrome region, contains two approximately 100-200 kb arrays of repeated small nucleolar (sno)RNAs processed from introns of long, paternally expressed non-protein-coding RNAs whose biogenesis and functions are poorly understood. We provide evidence that C/D snoRNAs do not derive from a single transcript as previously envisaged, but rather from (at least) two independent transcription units. We show that spliced snoRNA host-gene transcripts accumulate near their transcription sites as structurally constrained RNA species that are prevented from diffusing, as well as multiple stable nucleoplasmic RNA foci dispersed in the entire nucleus but not in the nucleolus. Chromatin structure at these repeated arrays displays an outstanding parent-of-origin-specific higher-order organization: the transcriptionally active allele is revealed as extended DNA FISH signals whereas the genetically identical, silent allele is visualized as singlet DNA FISH signals. A similar allele-specific chromatin organization is documented for snoRNA gene arrays at the imprinted Dlk1-Dio3 domain. Our findings have repercussions for understanding the spatial organization of gene expression and the intra-nuclear fate of non-coding RNAs in the context of nuclear architecture.

Iron loading increases ferroportin heterogeneous nuclear RNA and mRNA levels in murine J774 macrophages.

The transmembrane protein ferroportin is highly expressed in tissue macrophages, where it mediates iron export into the bloodstream. Although ferroportin expression can be controlled post-transcriptionally through a 5' iron-responsive element in its mRNA, various studies have documented increased ferroportin mRNA levels in response to iron, suggesting transcriptional regulation. We studied the effect of iron loading on levels of macrophage ferroportin mRNA, as well as heterogeneous nuclear RNA (hnRNA), the immediate product of ferroportin gene transcription. J774 cells, a mouse macrophage cell line, were incubated for 0, 3, 6, 9, 12, and 24 h in medium supplemented or not with 200 mumol/L iron. Quantitative RT-PCR was used to measure steady-state levels of ferroportin mRNA and hnRNA. Ferroportin mRNA levels increased by 12 h after iron treatment, reaching 6 times the control levels after 24 h. Changes in ferroportin mRNA levels were paralleled by similar changes in the levels of ferroportin hnRNA. Time course studies of ferroportin mRNA and hnRNA abundance after incubating cells with the transcriptional inhibitor actinomycin D revealed that ferroportin mRNA has a half-life of approximately 4 h and that iron loading does not stabilize ferroportin mRNA or hnRNA. Collectively, these data are consistent with the hypothesis that iron increases macrophage ferroportin mRNA levels by inducing transcription of the ferroportin gene.

Detection of genetic homogeneity of Panax notoginseng cultivars by sequencing nuclear 18S rRNA and plastid matK genes.

The nuclear 18S rRNA and chloroplast MATK genes of 18 samples of Panax notoginseng and its processed material Sanqi (Radix Notoginseng) were analyzed. The two genes, regardless of cultivar origin, were found to be identical to genotype R1 and M1, respectively, of the published sequences (GenBank accession no. D85171 and AB027526). This phenomenon implies that the species is highly conserved, which is probably caused by the use of the same strain in cultivation and the lack of active mutation in these two genes.

Molecular identification of Astragalus membranaceus at the species and locality levels.

Astragalus membranaceus (Fisch.) Bunge, a commonly used Chinese medicinal material, from certain localities contains more favourable trace elements and fewer harmful trace elements than those from other localities. Therefore, there is a need to distinguish Astragalus membranaceus from different localities. Internal transcribed spacer 1 (ITS1) of the nuclear ribosomal RNA gene of 23 Astragalus membranaceus samples were sequenced to confirm the species of the samples. Arbitrarily primed polymerase chain reaction (APPCR) was then used to obtain unique fingerprints for each sample using several primers. The presence and absence of bands were used for calculating mean similarity indexes among the samples. It was found that the Heilongjiang samples were markedly distinguishable from samples of other localities. In addition, bands common for samples from the same locality were also identified and used to distinguish samples from Neimengu and Shanxi. Therefore, Astragalus membranaceus from these provinces, the major cultivation places in China, can be differentiated.