Hoya pyrifolia (Apocynaceae), a new species from south-western Yunnan, China

Hoya pyrifolia, a new species of Apocynaceae from Yunnan Province, China, is described and illustrated. Results from phylogenetic analyses, based on combined DNA fragments of the nuclear ribosomal external transcribed spacer (ETS), intergeneric transcribed spacer (ITS) and three plastid DNA fragments (matK, psbA-trnH and trnT-trnL), showed that the new species was nested within a clade, including Hoya species distributed in the subtropical foothills of the Himalayas and the Tibet-Sichuan Plateau. Morphologically, the new species can be distinguished from its close relatives by its pyriform and slightly pubescent leaves, as well as the 4-flowered inflorescences.

Molecular Phylogeny of Axonopus (Poaceae, Panicoideae, Paspaleae): Monophyly, Synapomorphies, and Taxonomic Implications for Infrageneric Classification and Species Complexes

Axonopus P. Beauv. comprises nearly 90, mostly New World, species characterized by having spikelets with the inverse position (i.e., the backs of the upper glume and the upper lemma turned away from the rachis). The genus has been divided into four sections, five series, and three subseries, based exclusively on morphological features. Previous phylogenetic analyses based on a limited sampling of species showed Axonopus to be a monophyletic genus. In this study we increased the number of species sampled (46 species in the combined tree) and sequenced four DNA regions (external transcribed spacer [ETS], internal transcribed spacer [ITS], trnL-F, and ndhF). We tested the monophyly of Axonopus and its traditional infrageneric categories using parsimony, likelihood, and Bayesian inference. Additionally, we performed ancestral character state reconstructions of 45 morphological characters to infer autapomorphies of the species and synapomorphies for the genus and clades. Our findings confirmed Axonopus as a monophyletic genus only when Centrochloa Swallen and Ophiochloa Filg., Davidse & Zuloaga are included within it. Our analyses also showed that, with the exception of section Lappagopsis, infrageneric categories from previous classifications of the genus are artificial. Twenty-one morphological character states were identified as potential autapomorphies; two were reconstructed as potential synapomorphies for Axonopus, whereas 12 were reconstructed as potential synapomorphies for specific clades within the genus. Further molecular analyses, including sequencing of unlinked nuclear genes, are needed in order to reach a robust phylogenetic classification of the genus.

90S pre-ribosome transformation into the primordial 40S subunit

Production of small ribosomal subunits initially requires the formation of a 90S precursor followed by an enigmatic process of restructuring into the primordial pre-40S subunit. We elucidate this process by biochemical and cryo–electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90S pre-ribosome, followed by Utp24 endonuclease–driven RNA cleavage at site A1, thereby separating the 5′-external transcribed spacer (ETS) from 18S ribosomal RNA. Next, the 5′-ETS and 90S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40S emerges, still retaining some 90S factors including Dhr1, now ready to unwind the final small nucleolar U3–18S RNA hybrid. Our data shed light on the elusive 90S to pre-40S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.

NEW DISTRIBUTION REPORT ON THE ALIEN SPECIES ARTEMISIA VERLOTIORUM LAMOTTE (ASTERACEAE-ANTHEMIDEAE) FROM GILGIT-BALTISTAN REGION OF PAKISTAN

Artemisia verlotiorum Lamotte (Asteraceae), a species described from Europe but native to East Asia is an alien and/or invasive species grow naturally in many European regions, North and South Africa, South America, Australia, New Zealand and Western Asia. In continuance to our work on Northeastern Pakistani Artemisia, here we report the first local occurrence of verlotiorum Lamotte. from Gilgit-Baltistan region of Pakistan by investigating its geographical distribution and phylogenetic analysis. To date, we have observed the species in stony landscapes of Ghizer district of Gilgit-Baltistan. Phylogenetic analysis of Northeastern Pakistani A. verlotiorum with maximum likelihood approach using its internal transcribed spacer (ITS) and external transcribed spacer (ETS) of nuclear ribosomal DNA (nrDNA) sequences showed its resemblance with other Artemisia species reported from different parts of the world. This species needs to be included in the rare plant species list in the flora of Pakistan and immediate conservative approaches should be adopted to impede its extinction from the country.

Modification of Adenosine196 by Mettl3 Methyltransferase in the 5’-External Transcribed Spacer of 47S Pre-rRNA Affects rRNA Maturation

Ribosome biogenesis is among the founding processes in the cell. During the first stages of ribosome biogenesis, polycistronic precursor of ribosomal RNA passes complex multistage maturation after transcription. Quality control of preribosomal RNA (pre-rRNA) processing is precisely regulated by non-ribosomal proteins and structural features of pre-rRNA molecules, including modified nucleotides. However, many participants of rRNA maturation are still unknown or poorly characterized. We report that RNA m6A methyltransferase Mettl3 interacts with the 5′ external transcribed spacer (5′ETS) of the 47S rRNA precursor and modifies adenosine 196. We demonstrated that Mettl3 knockdown results in the increase of pre-rRNA processing rates, while intracellular amounts of rRNA processing machinery components (U3, U8, U13, U14, and U17 small nucleolar RNA (snoRNA)and fibrillarin, nucleolin, Xrn2, and rrp9 proteins), rRNA degradation rates, and total amount of mature rRNA in the cell stay unchanged. Increased efficacy of pre-rRNA cleavage at A’ and A0 positions led to the decrease of 47S and 45S pre-rRNAs in the cell and increase of mature rRNA amount in the cytoplasm. The newly identified conserved motif DRACH sequence modified by Mettl3 in the 5′-ETS region is found and conserved only in primates, which may suggest participation of m6A196 in quality control of pre-rRNA processing at initial stages demanded by increased complexity of ribosome biogenesis.

Radiations of fairy-aprons (Utricularia dichotoma, Lentibulariaceae) in Australia and New Zealand: molecular evidence and proposal of new subspecies

The Utricularia dichotoma Labill. complex is a morphologically and ecologically variable group of closely related taxa with a mostly temperate distribution across New Zealand, New Caledonia and Australia. Taxonomic boundaries within the complex have been the subject of speculation, with several previously recognised species being synonymised after a nomenclatural revision. We sampled 296 populations representing all known taxa; 223 accessions were used in the full phylogenetic analysis based on two non-coding chloroplast regions (rps16, trnD–T) and two nuclear ribosomal spacers (external transcribed spacer, ETS; internal transcribed spacer-1, ITS-1), whereas the remaining accessions were identified by using ITS-1 barcodes. We found strong support for a paraphyletic U. dichotoma, with accessions matching the type material of that name grouped within a polytomy that includes clades containing accessions of U. monanthos Hook.f and U. novae-zelandiae Hook.f. Specific statuses for five recently described species previously included in U. dichotoma s.l. do not fall within this polytomy, nor do the two species U. oppositiflora R.Br. and U. speciosa R.Br. resurrected from synonymy of U. dichotoma. All sampled accessions from New Zealand form a single clade within U. dichotoma as recognised here. We here propose that seven clades recovered here be recognised as subspecies, and describe eight new subspecies, including two new combinations. We also propose that the monophyletic clade sister to U. beaugleholei Gassin be assigned to subspecies rank under that name.

The Hordeum bulbosum 25S-18S rDNA region: comparison with Hordeum vulgare and other Triticeae

Hordeum vulgare and Hordeum bulbosum are two closely related barley species, which share a common H genome. H. vulgare has two nucleolar organizer regions (NORs), while the NOR of H. bulbosum is only one. We sequenced the 2.5 kb 25S-18S region in the rDNA of H. bulbosum and compared it to the same region in H. vulgare as well as to the other Triticeae. The region includes an intergenic spacer (IGS) with a number of subrepeats, a promoter, and an external transcribed spacer (5′ETS). The IGS of H. bulbosum downstream of 25S rRNA contains two 143-bp repeats and six 128-bp repeats. In contrast, the IGS in H. vulgare contains an array of seven 79-bp repeats and a varying number of 135-bp repeats. The 135-bp repeats in H. vulgare and the 128-bp repeats in H. bulbosum show similarity. Compared to H. vulgare, the 5′ETS of H. bulbosum is shorter. Additionally, the 5′ETS regions in H. bulbosum and H. vulgare diverged faster than in other Triticeae genera. Alignment of the Triticeae promoter sequences suggests that in Hordeum, as in diploid Triticum, transcription starts with guanine and not with adenine as it is in many other plants.

Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit

More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5′ external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5′ ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.

Conformational switches control early maturation of the eukaryotic small ribosomal subunit

Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5’ external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5’ external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5’ external transcribed spacer ribonucleoprotein – provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly.