Complete chloroplast genome sequencing of Caralluma quadrangula and comparative analysis of the Asclepiadoideae subfamily (Apocynaceae)

Caralluma quadrangula is an herbaceous plant distributed in Saudi Arabia, India, Africa, and the Canary Islands. To assess the phylogenetic and evolutionary relationships among the Asclepiadoideae subfamily in the Apocynaceae family, we carried out a compara-tive chloroplast (cp) genome analysis of four species. The size of the C. quadrangula chloroplast genome is 161,456 bp, while the large single-copy (LSC) is 85,992 bp, the small single-copy (SSC) is 13,380 bp, and the two inverted repeats (IRs) are 31,042 bp each. The genome has a total of 129 genes, among which 19 are located at the inverted repeat region, 85 are protein coding genes, 36 are tRNA genes, and eight are rRNA genes. Visualization of single-copy and inverted repeat borders showed that expansion and contraction have occurred in the cp genomes of the compared species of Ascle-piadoideae. The genome comparative analysis shows that the coding regions are more highly conserved than the non-coding region; thus, the variable hotspot can serve as a barcode for species in the subfamily. Phylogenetic analysis conducted based on cp sequences identified Stapelia as sister to Caralluma, in agreement with previous studies. The current study may facilitate the development of molecular markers to ease the identifi cation and authentication of members of the genus Caralluma in the Apocynaceae

Агрессивная форма ювенильной макромастии

ПОДРОСТКИМОЛОЧНЫЕ ЖЕЛЕЗЫ ЧЕЛОВЕКА /АНОМАЛБОЛЕЗНИ РЕДКИЕМАКРОМАСТИЯГИПЕРТРОФИЯМОЛОЧНОЙ ЖЕЛЕЗЫ ПЛАСТИКАХИРУРГИЧЕСКИЕ ОПЕРАЦИИ ВОССТАНОВИТЕЛЬНЫЕМОЛОЧНОЙ ЖЕЛЕЗЫ БОЛЕЗНИ /ТЕР /ХИ

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

Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis

Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa

Insights into the phylogenetic relationship of the lamiids orders based on whole chloroplast genome sequencing

Lamiids, an asterid clade consists of over 40,000 species distributed among eight orders, Icacinales, Garryales and Metteniusales, known informally as “basal lamiids”, Boraginales, Gentianales, Lamiales, Solanales, and Vahliales, known informally as “core lamiids”. Over recent years, different phylogenetic studies have clarified the formation of lamiids, however, the relationships among the orders remain unresolved. The whole chloroplast genome sequences of 49 taxa have been downloaded from GenBank (NCBI) and used to evaluate the evolutionary relationships of lamiids, and particularly to test the relationships among the main lineages of lamiids. The phylogenetic tree resulting from using Maximum Parsimony and Bayesian Inference were with identical topologies and provide good support for the following relationships, Lamiales as sister to Solanales, and Boraginales as sister to Gentianales together forming the core lamiids. In basal lamiids, the result support Garryales as sister to Metteniusales, while Icacinales was found to be the immediate sister to the other orders in the core lamiids. Our results may improve our understanding of the relationships between the orders of lamiids

Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution

This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family

Ecological assessment of heavy metals in the grey mangrove (Avicennia marina) and associated sediments along the Red Sea coast of Saudi Arabia

Summary: Mangroves play an integral role as a metal accumulator in tropical and subtropical marine ecosystems. Twenty-one sets of sediment samples and portions of mangroves were collected along the Saudi Arabian coast of the Red Sea to assess the accumulation and ecological risks of heavy metals. Results showed that the following mean concentrations of heavy metals in sediments: Cr (46.14 μg g−1 ± 18.48) > Cu (22.87 μg g−1 ± 13.60) > Ni (21.11 μg g−1 ± 3.2) > Pb (3.82 μg g−1 ± 2.46) > Cd (0.75 μg g−1 ± 0.87). The maximum concentrations of the studied metals were above the threshold effect level, indicating a limited impact on the respective ecosystems. The maximum concentration of Cd exceeded its toxic effect threshold, revealing a harmful risk to biota in the sediments. Based on metallo-phytoremedation, biological concentration factors were >1, suggesting that Avicennia marina can accumulate heavy metals, especially Cr and Pb. The translocation factor was above the known worldwide average. The geo-accumulation index revealed that sediments in mangrove areas ranged from moderately to heavily contaminated with Cd at Al-Haridhah and moderately contaminated at South Jeddah, Rabigh, Duba, and the wastewater treatment station near Jazan. The ecological risk index revealed that Cd could pose a relatively very high risk to the mangrove ecosystem. The present study emphasized the possibility of establishing a framework for the management of the coastal aquatic ecosystems along the Red Sea coast of Saudi Arabia. Keywords: Mangrove, Avicennia marina, Heavy metals, Pollution indices, Sediment quality, Red Se

The complete chloroplast genome of Blepharis ciliaris (Acanthaceae)

Blepharis ciliaris is an important medicinal plant and endemic species in Saudi Arabia. This study reported the complete chloroplast genome of B. ciliaris, the second to be sequence in non cystolith clade of Acanthaceae. The genome is 149, 717 bp in size and consisted of a pair of inverted repeat (25, 331 bp each) separating the two single copy region, the large single copy (LSC) 82, 057 bp and small single copy SSC 16, 998 bp. The plastome has overall GC content of 38.5% and 112 genes comprising of 79 protein coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic relationship analysis showed that B. ciliaris is sister to Aphelandra knappiea. The cp genome reported in this study will useful in genetic diversity and evolutionary studies of the species

Teaching and Learning Computer Science at Al Baha University, Saudi Arabia : Insights from a staff development course

In this special session we meet a set of projects in computer science and engineering education at a university in Saudi Arabia. They are the product of a pedagogical development course ran in collaboration with a Swedish university during the academic year 2013/2014. The projects reflect the local situation, with its possibilities and challenges, and suggest steps to take, in the local environment, to enhance education. As such it is a unique document that brings insights from computer science and engineering education into the international literature