Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

/pdf/sequencing-of-allotetraploid-cotton-gossypium-hirsutum-l-acc-3aex1man4n.pdf

Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

/pdf/evolution-of-gene-duplication-in-plants-rtuaqmb3s9.pdf

Evolution of Gene Duplication in Plants.

Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

/pdf/genome-sequence-of-cultivated-upland-cotton-gossypium-4wnt07e5c8.pdf

Genome sequence of cultivated Upland cotton ( Gossypium hirsutum TM-1) provides insights into genome evolution

The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

/pdf/gene-duplication-and-evolution-in-recurring-polyploidization-1tk6fsc37e.pdf

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Water scarcity is a global issue and the application of untreated wastewater for irrigation is a general practice in developing countries. Major drawbacks of wastewater irrigation include the presence of heavy metals and disease-causing bacterial pathogens. The present study was conducted for identification of the bacterial strains in wastewater and wastewater irrigated vegetable and crops. XLT-4 cultural media was used for culture-based detection of different bacterial pathogens (red with black center for Salmonella, yellowish for E. coli and small pink colonies for Shigella). The presence of these diseasecausing pathogens was indicated in almost all samples. For further confirmation, microscopic analysis was performed, which showed gram negative rod shaped colonies. Various biochemical identification tests (catalase, urease, oxidase and lactase) also confirmed the presence of pathogenic bacterial species in analyzed samples. PCR based diagnosis was carried out using species specific primers for Mdh gene of E. coli, IpaB gene of Salmonella and IpaH gene of Shigella. 16s rRNA was amplified in all observed samples as positive control. The Mdh gene amplification was observed in wastewater, pumpkin, sugarcane, maize, brinjal, lettuce, spinach, cabbage and radish samples, while IpaB gene was amplified *e-mail: shameemraja@gcwuf.edu.pk DOI: 10.15244/pjoes/145605 ONLINE PUBLICATION DATE:

Physicochemical, Molecular and Cultural
Identification of Microbial Pathogens
in Wastewater Irrigated Crops

WITHDRAWN: Circulation of dengue virus serotypes in hyperendemic region of New Delhi, India during 2011-2017

Diabetes and its related complications are considered as one of the major causes of morbidity and mortality round the globe [1]. Diabetes is a noncommunicable metabolic syndrome may either characterized by defective or decreased level of insulin secretion [2]. The current estimate on global diabetes epidemiology reveals that roughly under half of billion population is affected by diabetes and associated pathologies and is projected to increase by around 50% by 2045 [3].

MRSA, EBSL, and Biofilm Formation in Diabetic Foot Ulcer Infections

Essential oils (EOs) have been reported as a promising group of naturally extracted compounds due to their various reported biological activities. Ipomoea carnea is a widely distributed plant with many traditional uses worldwide. However, although the EOs of various Ipomea species have been reported, I. carnea remains poorly studied. Therefore, the present investigation aimed to characterize the chemical profile of the EO of I. carnea growing in Egypt via gas chromatography/mass spectroscopy (GC-MS) and correlate its profile with other reported species via chemometric analysis using agglomerative hierarchical clustering (AHC) and principal component analysis (PCA). In addition, the aim was to determine the antioxidant and antibacterial activities of the extracted EO. Depending on the GC-MS analysis, 31 compounds were identified, mainly terpenes (94.82), with traces of carotenoid and apocarotenoid-derived compounds. The major compounds were tau-cadinol (35.68%), α-cadinol (26.76%), spathulenol (8.11%), and caryophyllene oxide (6.56%), which were assigned as major compounds. The chemometric studies showed that the Egyptian ecospecies of I. carnea differs in chemical profile from those growing in Brazil, as well as those reported for other Ipomea species. The EO showed significant DPPH and ABTS radical scavenging abilities, with IC50 values of 33.69 and 40.86 mg L−1, respectively. Additionally, the I. carnea EO displayed significant inhibition against the growth of all tested bacterial strains, where it showed an MIC range of 82–1442 mg mL−1. Based on the current results, the I. carnea EO, particularly the major identified compounds, could be used as a potential eco-friendly green resource for antioxidant and antimicrobial activities. Therefore, further study is recommended to evaluate the biological significance of the main compounds, either individually or in combination, as well as assess their modes of action and safety.

/pdf/essential-oil-of-ipomoea-carnea-chemical-profile-chemometric-3c7herr9.pdf

Salman Alamery

Papers

Physicochemical, Molecular and Cultural Identification of Microbial Pathogens in Wastewater Irrigated Crops

WITHDRAWN: Circulation of dengue virus serotypes in hyperendemic region of New Delhi, India during 2011-2017

MRSA, EBSL, and Biofilm Formation in Diabetic Foot Ulcer Infections

Essential Oil of Ipomoea carnea: Chemical Profile, Chemometric Analysis, Free Radical Scavenging, and Antibacterial Activities