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Salman Alamery

Bio: Salman Alamery is an academic researcher from King Saud University. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 14, co-authored 57 publications receiving 1823 citations. Previous affiliations of Salman Alamery include Australian Centre for Plant Functional Genomics & Center for Excellence in Education.

Papers published on a yearly basis

Papers
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Journal ArticleDOI
Boulos Chalhoub1, Shengyi Liu2, Isobel A. P. Parkin3, Haibao Tang4, Haibao Tang5, Xiyin Wang6, Julien Chiquet1, Harry Belcram1, Chaobo Tong2, Birgit Samans7, Margot Correa8, Corinne Da Silva8, Jérémy Just1, Cyril Falentin9, Chu Shin Koh10, Isabelle Le Clainche1, Maria Bernard8, Pascal Bento8, Benjamin Noel8, Karine Labadie8, Adriana Alberti8, Mathieu Charles9, Dominique Arnaud1, Hui Guo6, Christian Daviaud, Salman Alamery11, Kamel Jabbari12, Kamel Jabbari1, Meixia Zhao13, Patrick P. Edger14, Houda Chelaifa1, David C. Tack15, Gilles Lassalle9, Imen Mestiri1, Nicolas Schnel9, Marie-Christine Le Paslier9, Guangyi Fan, Victor Renault16, Philippe E. Bayer11, Agnieszka A. Golicz11, Sahana Manoli11, Tae-Ho Lee6, Vinh Ha Dinh Thi1, Smahane Chalabi1, Qiong Hu2, Chuchuan Fan17, Reece Tollenaere11, Yunhai Lu1, Christophe Battail8, Jinxiong Shen17, Christine Sidebottom10, Xinfa Wang2, Aurélie Canaguier1, Aurélie Chauveau9, Aurélie Bérard9, G. Deniot9, Mei Guan18, Zhongsong Liu18, Fengming Sun, Yong Pyo Lim19, Eric Lyons20, Christopher D. Town5, Ian Bancroft21, Xiaowu Wang, Jinling Meng17, Jianxin Ma13, J. Chris Pires22, Graham J.W. King23, Dominique Brunel9, Régine Delourme9, Michel Renard9, Jean-Marc Aury8, Keith L. Adams15, Jacqueline Batley11, Jacqueline Batley24, Rod J. Snowdon7, Jörg Tost, David Edwards24, David Edwards11, Yongming Zhou17, Wei Hua2, Andrew G. Sharpe10, Andrew H. Paterson6, Chunyun Guan18, Patrick Wincker1, Patrick Wincker25, Patrick Wincker8 
22 Aug 2014-Science
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

1,743 citations

Journal ArticleDOI
TL;DR: In this article, Salicylic acid and proline treatments led to increased stem length, plant dry weights, chlorophyll concentration, relative water content, activity of antioxidant enzymes, and grain yield under drought stress.
Abstract: Barley is a very important crop worldwide and has good impact in preserving food security. The impacts of 10 mM proline and 0.5 mM salicylic acid were evaluated on water stressed barley plants (Hordeum vulgare L. Giza126). Salicylic acid and proline treatments led to increased stem length, plant dry weights, chlorophyll concentration, relative water content, activity of antioxidant enzymes, and grain yield under drought stress. Nevertheless, lipid peroxidation, electrolyte leakage (EL), superoxide (O2·−), and hydrogen peroxide (H2O2) significantly decreased in treated barley plants with proline and salicylic acid in both growing seasons as compared with drought treatment only, which caused significant decrease in stem length, plant dry weights, chlorophyll concentration, activity of antioxidant enzymes, as well as biological and grain yield. These results demonstrated the importance of salicylic acid and proline as tolerance inducers of drought stress in barley plants.

89 citations

Journal ArticleDOI
29 Apr 2020-Agronomy
TL;DR: In this paper, the impact of biochar and chitosan on barley plants under drought stress conditions was investigated during two field experiments, and the results confirmed that drought stress negatively affected morphological and physiological growth traits of barley plants such as plant height, number of leaves, chlorophyll concentrations, and relative water content.
Abstract: The impact of biochar and chitosan on barley plants under drought stress conditions was investigated during two field experiments. Our results confirmed that drought stress negatively affected morphological and physiological growth traits of barley plants such as plant height, number of leaves, chlorophyll concentrations, and relative water content. However, electrolyte leakage (EL%), lipid peroxidation (MDA), soluble sugars, sucrose and starch contents significantly increased as a response to drought stress. Additionally, 1000 grain weight, grains yield ha−1 and biological yield significantly decreased in stressed barley plants, also anatomical traits such as upper epidermis, lower epidermis, lamina, and mesophyll tissue thickness as well as vascular bundle diameter of flag leaves significantly decreased compared with control. The use of biochar and chitosan led to significant increases in plant height, number of leaves, and chlorophyll concentrations as well as relative water content; nevertheless these treatments led to significant decreases in electrolyte leakage (EL%) and lipid peroxidation (MDA) in the stressed plants. Moreover, anatomical and yield characters of stressed barley plants were improved with application of biochar and chitosan. The results proved the significance of biochar and chitosan in alleviating the damaging impacts of drought on barley plants.

82 citations

Journal ArticleDOI
TL;DR: The results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.
Abstract: An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

74 citations

Journal ArticleDOI
TL;DR: Conformational changes were suggested in the BSA on its interaction with poziotinib based on fluorescence experimental data and the binding constant for BSA-poziot inib showed a maximum decrease in presence of quercetin followed by naringenin, rutin and sinapic acid respectively.

49 citations


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TL;DR: 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 subgenomes, suggesting asymmetric evolution.
Abstract: 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.

1,221 citations

Journal ArticleDOI
TL;DR: This review surveys 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.
Abstract: 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.

856 citations

Journal ArticleDOI
TL;DR: A draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map is produced for G. hirsutum, revealing conserved gene order and concerted evolution of different regulatory mechanisms for Cellulose synthase and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 may be important for enhanced fiber production.
Abstract: 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.

836 citations

Journal ArticleDOI
TL;DR: A comprehensive landscape of different modes of gene duplication across the plant kingdom is identified by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
Abstract: 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.

461 citations

Journal ArticleDOI
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes resource, with a focus on recent developments and expansions, including the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data.
Abstract: 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.

409 citations