Complete Sequences of Organelle Genomes from the Medicinal Plant Rhazya Stricta (Apocynaceae) and Contrasting Patterns of Mitochondrial Genome Evolution Across Asterids

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. Results: The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Conclusions: Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications.King Abdulaziz UniversityIntegrative Biolog

Transcriptomic and metabolic responses of Calotropis procera to salt and drought stress

Background: Calotropis procera is a wild plant species in the family Apocynaceae that is able to grow in harsh, arid and heat stressed conditions. Understanding how this highly adapted plant persists in harsh environments should inform future efforts to improve the hardiness of crop and forage plant species. To study the plant response to droμght and osmotic stress, we treated plants with polyethylene glycol and NaCl and carried out transcriptomic and metabolomics measurements across a time-course of five days. Results: We identified a highly dynamic transcriptional response across the time-course including dramatic changes in inositol signaling, stress response genes and cytokinins. The resulting metabolome changes also involved sharp increases of myo-inositol, a key signaling molecule and elevated amino acid metabolites at later times. Conclusions: The data generated here provide a first glimpse at the expressed genome of C. procera, a plant that is exceptionally well adapted to arid environments. We demonstrate, through transcriptome and metabolome analysis that myo-inositol signaling is strongly induced in response to drought and salt stress and that there is elevation of amino acid concentrations after prolonged osmotic stress. This work should lay the foundations of future studies in adaptation to arid environments

Transcriptional analysis of Rhazya stricta in response to jasmonic acid

Background: Jasmonic acid (JA) is a signal transducer molecule that plays an important role in plant development and stress response; it can also efficiently stimulate secondary metabolism in plant cells. Results: RNA-Seq technology was applied to identify differentially expressed genes and study the time course of gene expression in Rhazya stricta in response to JA. Of more than 288 million total reads, approximately 27% were mapped to genes in the reference genome. Genes involved during the secondary metabolite pathways were up- or downregulated when treated with JA in R. stricta. Functional annotation and pathway analysis of all up- and downregulated genes identified many biological processes and molecular functions. Jasmonic acid biosynthetic, cell wall organization, and chlorophyll metabolic processes were upregulated at days 2, 6, and 12, respectively. Similarly, the molecular functions of calcium-transporting ATPase activity, ADP binding, and protein kinase activity were also upregulated at days 2, 6, and 12, respectively. Time-dependent transcriptional gene expression analysis showed that JA can induce signaling in the phenylpropanoid and aromatic acid pathways. These pathways are responsible for the production of secondary metabolites, which are essential for the development and environmental defense mechanism of R. stricta during stress conditions. Conclusions: Our results suggested that genes involved in flavonoid biosynthesis and aromatic acid synthesis pathways were upregulated during JA stress. However, monoterpenoid indole alkaloid (MIA) was unaffected by JA treatment. Hence, we can postulate that JA plays an important role in R. stricta during plant development and environmental stress conditions. How to cite: Hajrah, NH, Rabah SO, Alghamdi MK, et al. Transcriptional analysis of Rhazya stricta in response to jasmonic acid. Electron J Biotechnol 2021;50. https://doi.org/10.1016/j.ejbt.2021.01.00

Analysis of transcriptional response to heat stress in Rhazya stricta

Clusters of assembled transcripts of R. stricta SRA in mature leaves (A5-L8) at different time points of the day (A, morning; F-H, midday & L, dusk). Grey lines indicate expression patterns of individual transcripts in a given cluster. Blue lines indicate overall expression pattern across different transcripts of a given cluster. (PDF 397 kb

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Transcriptomic analysis of salt stress responsive genes in Rhazya stricta.

Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl) across four time intervals (0, 2, 12 and 24 h) to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR) proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS) production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged

New Insights into Plagiogrammaceae (Bacillariophyta) Based on Multigene Phylogenies and Morphological Characteristics with the Description of a New Genus and Three New Species

<div><p>Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies of the Plagiogrammaceae were inferred but included only up to six genera: <i>Plagiogramma</i>, <i>Dimeregramma</i>, <i>Neofragilaria</i>, <i>Talaroneis</i>, <i>Psammogramma</i> and <i>Psammoneis</i>. In this paper, we describe a new plagiogrammoid genus, <i>Orizaformis</i>, obtained from Bohai Sea (China) and present molecular phylogenies of the family based on three and four genes (nuclear-encoded large and small subunit ribosomal RNAs and chloroplast-encoded <i>rbc</i>L and <i>psb</i>C). Also included in the new phylogenies is <i>Glyphodesmis</i>. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of <i>Talaroneis</i>, <i>Orizaformis</i> and <i>Psammoneis</i>, and the second of <i>Glyphodesmis</i>, <i>Psammogramma</i>, <i>Neofragilaria</i>, <i>Dimeregramma</i> and <i>Plagiogramma</i>. In addition, we describe three new species within established genera: <i>Psammoneis obaidii</i>, which was collected from the Red Sea, Saudi Arabia; and <i>Neofragilaria stilus</i> and <i>Talaroneis biacutifrons</i> from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: <i>Neofragilaria anomala</i> and <i>Neofragilaria lineata</i>. Our observations suggest that the biodiversity of the family is strongly needed to be researched, and the phylogenetic analyses provide a useful framework for future studies of Plagiogrammaceae.</p></div

<i>Neofragilaria stilus</i>, LM (a-b) and SEM (f-g).

<p>Cultured material SZCZM116. (a) Zigzag colony linked by valve corners, frustule rectangular in girdle view, two plastids per cell. (b) Cleaned material in valve view, linear to lanceolate, robust striae. (c) Exterior view of natural sample, showing elaborate cribra and marginal spines. (d) Interior view of natural sample, a robust sternum, rimoportulae absent. (e) Exterior view in culture, showing corroded cribra and slit-like areolae in the apical pore field. (f) Interior view, rimoportulae absent. (g) Chain colony in girdle view and plain girdle bands.</p

Maximum likelihood phylogeny of 26 strains of Plagiogrammacean diatoms (with bootstrap values at nodes) was inferred from four markers (LSU, SSU rDNA, <i>rbc</i>L and <i>psb</i>C).

<p>Taxa (<i>Neofragilaria stilus</i>, <i>Orizaformis holarctica</i> and <i>Psammoneis obaidii</i>) in bold are newly described species. Support values lower than 50% were omitted. The outgroup <i>Asterionella formosa</i> was removed from the tree.</p

<i>Neofragilaria anomala</i>, drawings (Fig a), LM (b-f) and SEM (g-k).

<p>(a) Valve view, drawings of Malcolm Giffen, without scale. (b) Scan of illustrations from Desikachary et al (1987), showing robust striae and a distinct sternum. (c-f) Valve view, showing robust striae and a distinct sternum. These images were taken from Slide Br 426/52 of Malcolm Giffen depsoited in Hustedt Diatom Collection at Alfred Wegener Institute in Bremerhaven. (g-i) External view, based on clean material SZCZ16502 of natural samples from Juan de Nova in Mozambique Channel deposited in Palaeoceanology Unit, Faculty of Geosciences, University of Szczecin. (j) Internal view, the material is the same as Fig 6g–6i. (k) Incomplete girdle band (see arrow), the material is the same as Fig 6g–6i.</p