35 results on '"Sarwar, Azam"'
Search Results
2. Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds
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Neelam A. Topno, Veerbhan Kesarwani, Sandeep Kumar Kushwaha, Sarwar Azam, Mohammad Kadivella, Ravi Kumar Gandham, and Subeer S. Majumdar
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milk fat ,whole-genome sequencing ,SNPs ,genomic variation ,variant calling ,indigenous breeds ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The effect of breed on milk components—fat, protein, lactose, and water—has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3, and NT5E. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
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- 2023
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3. Living ghosts and the Laapata: the episode of genocide continuum in Pakistani art.
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Sarwar, Azam
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PAKISTANI art , *GENOCIDE , *WAR on Terrorism, 2001-2009 , *POLITICAL change - Abstract
The systematic disappearance of individuals is very much a global phenomenon. In Pakistan, this phenomenon re-emerged after Pakistan decided to get involved in the U.S.-led 'war on terror' in the wake of 9/11. This paper exposes the politics of necropolitics in Pakistan through art, as death plays a significant role in setting up a political change. I contend that Ramla Fatima's artworks put a human face to death and speak truth to power, to draw on Foucault, interlinking death with politics to expose the hiding and camouflaging of death in Pakistan. Fatima's artworks represent another episode of the genocide continuum in Pakistan – the unending enforced disappearances and the sufferings of the families of the laapata – the disappeared. By painting necropolitics, she transgresses the silencing culture, a legacy of enforced disappearances. Through art, she illustrates how victims and their families are condemned to a state of subalternity and ambiguity – ambiguous loss, slow violence and torture, and psychological scars. Her artworks also draw attention to the role of expressive art in evoking awareness of human rights violations and establishing the fact that the laapata's lives matter. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Transgression and transcendence in Shoaib Mansoor's feminist trilogy.
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Sarwar, Azam
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WOMEN'S empowerment , *FEMININITY , *FEMINISTS , *COLLECTIVE representation , *OTHER (Philosophy) - Abstract
This article examines Shoaib Mansoor's cult feminist trilogy—Khuda Kay Liye (2007), Bol (2011), Verna (2017)—to demonstrate how his transgressive heroines transgress myths of femininity, for example, those pertaining to Otherness, division, and the eternal feminine. Mansoor features transgressive heroines who transcend the patriarchal boundaries structured to contain them and challenge the voice of male authority. His heroines' transgressions thus take agency as the driving force for pursuing self-fulfilment in transcendence, undermining the domineering traits of patriarchy embedded in the status quo and herd values. The article adumbrates Pakistani cinema's transitional odyssey from women as docile bodies to transcendent agents by analyzing heroines' portrayals in traditional Pakistani cinema. I argue that Mansoor's feminist trilogy significantly contributes to women's cinema by addressing the audience as a woman and concerning with women. As Mansoor persuasively features transgressive heroines, watching the feminist trilogy as counter-narrative provides us with the representation of women as social subjects whose transformative actions destabilize discursive formations, accomplish transcendence, and create a space of woman empowerment. [ABSTRACT FROM AUTHOR]
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- 2023
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5. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India
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Sarwar Azam, Sashi Bhushan Rao, Padmaja Jakka, Veera NarasimhaRao, Bindu Bhargavi, Vivek Kumar Gupta, and Girish Radhakrishnan
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Genetics ,QH426-470 - Abstract
Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis.
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- 2016
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6. Transgression and transcendence in Shoaib Mansoor’s feminist trilogy
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Sarwar, Azam, primary
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- 2022
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7. Semiotics of Exile in Photography, Intersectional Racism and Epistemic Violence in Natasha Trethewey
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Zeng, Hong, primary and Sarwar, Azam, additional
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- 2021
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8. Breaking free from patriarchal appropriation of sacred texts: An Islamic feminist critique ofBol
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Sarwar, Azam, primary and Zeng, Hong, additional
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- 2021
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9. Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551
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Sarwar Azam, Chhaya Singh, Dayananda Siddavattam, Sunil Parthasarathy, and Shakti Kumar
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plasmids ,mobile elements ,genome sequence ,Biology ,Genome ,biodegradation ,Sphingobium ,03 medical and health sciences ,Plasmid ,Genetics ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,030304 developmental biology ,Genomic organization ,Whole genome sequencing ,organophosphate hydrolase ,0303 health sciences ,Whole Genome Sequencing ,030306 microbiology ,Molecular Sequence Annotation ,biology.organism_classification ,Genome Report ,Sphingomonadaceae ,Horizontal gene transfer ,horizontal gene transfer ,Mobile genetic elements ,GC-content ,Genome, Bacterial - Abstract
Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.
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- 2019
10. Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
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Himabindu Kudapa, Sarwar Azam, Andrew G Sharpe, Bunyamin Taran, Rong Li, Benjamin Deonovic, Connor Cameron, Andrew D Farmer, Steven B Cannon, and Rajeev K Varshney
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Medicine ,Science - Abstract
A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
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- 2014
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11. An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.
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Sarwar Azam, Abhishek Rathore, Trushar M Shah, Mohan Telluri, BhanuPrakash Amindala, Pradeep Ruperao, Mohan A V S K Katta, and Rajeev K Varshney
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Medicine ,Science - Abstract
Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.
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- 2014
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12. Designing of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches
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Mohd Abdullah, Mohammad Kadivella, Rolee Sharma, Syed M. Faisal, and Sarwar Azam
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Bacterial adhesin ,Antigenicity ,Leptospira ,medicine.medical_treatment ,Immunogenicity ,Reverse vaccinology ,medicine ,Computational biology ,Biology ,biology.organism_classification ,Adjuvant ,Epitope ,Cellular localization - Abstract
Leptospira is a zoonotic pathogen causing significant morbidity and mortality both in animals and humans. Although several surface proteins have been identified as vaccine candidate, they failed to induce sterilizing immunity and cross protection against different serovars. Thus, identification of highly immunogenic antigens that are conserved among pathogenic serovars would be first step towards development of universal vaccine for Leptospirosis. Here we used reverse vaccinology pipeline to screen core genome of pathogenic Leptospira spp.in order to identify suitable vaccine candidates. Based on properties like sub cellular localization, adhesin, homology to human proteins, antigenicity and allergenicity, 18 antigenic proteins were identified and were further investigated for immunological properties. Based on immunogenicity, Protegenicity, Antigenicity, B-cell and promiscuous T-cell epitopes, 6 Potential Vaccine Candidates (PVCs) were finally selected which covered most of the affected world population. For designing a Multi-Epitope Vaccine (MEV), 6 B-cell and 6 promiscuous MHC-I and MHC-II epitopes from each candidate were clustered with linkers in between and stitched along with a TLR4 adjuvant (APPHALS) at the N-terminal to form a construct of 361 amino acids. The physiochemical properties, secondary and tertiary structure analysis revealed that MEV was highly stable. Molecular docking analysis revealed the deep binding interactions of the MEV construct within the grooves of human TLR4 (4G8A). In-silico codon optimization and cloning of the vaccine construct assured good expression. Further, immune simulations have shown that MEV could induce strong and diverse B and T cell responses. Taken together our results indicate that the designed MEV could be a promising subunit vaccine candidate against Leptospirosis, however it requires experimental validation.
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- 2021
13. Comparative analysis of whole genome sequences of Leptospira spp. from RefSeq database provide interspecific divergence and repertoire of virulence factors
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Sarwar Azam, Rolee Sharma, Mohd Abdullah, Mohammad Kadivella, Mirza S. Baig, and Syed M. Faisal
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Comparative genomics ,Database ,Leptospira ,RefSeq ,Pan-genome ,Virulence ,Mobilome ,Biology ,biology.organism_classification ,computer.software_genre ,Clade ,computer ,Genome - Abstract
Leptospirosis is an emerging zoonotic and neglected disease across the world causing huge loss of life and economy. The disease is caused by Leptospira of which 605 sequenced genomes representing 72 species are available in RefSeq database. A comparative genomics approach based on Average Amino acid Identity (AAI), Average Nucleotide Identity (ANI), and Insilco DNA-DNA hybridization provide insight that taxonomic and evolutionary position of few genomes needs to be changed and reclassified. Clustering on the basis of AAI of core and pan-genome contradict clustering pattern on basis of ANI into 4 clusters. Amino acid identity based hierarchical clustering clearly established 3 clusters of Leptospira correlating with level of virulence. Whole genome tree supported three cluster classifications and grouped Leptospira into three clades termed as pathogenic, intermediate and saprophytic. Leptospira genus consist of diverse species and exist in heterogeneous environment, it contains relatively large and closed core genome of 1038 genes. Analysis provided pan genome remains open with 20822 genes. COG analysis revealed that mobilome related genes were found mainly in pan-genome of pathogenic clade. Clade specific genes mined in the study can be used as marker for determining clade and associating level of virulence of any new Leptospira species. Many known Leptospira virulent genes were absent in set of 78 virulent factors mined using Virulence Factor database. A deep search approach provided a repertoire of 496 virulent genes in pan-genome. Further validation of virulent genes will help in accurately targeting pathogenic Leptospira and controlling leptospirosis.Graphical Abstract
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- 2021
14. Genetic Characterization and Comparative Genome Analysis ofBrucella melitensisIsolates from India
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Sashi Bhushan Rao, Sarwar Azam, Veera NarasimhaRao, Padmaja Jakka, Bindu Bhargavi, Girish K. Radhakrishnan, and Vivek Kumar Gupta
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0301 basic medicine ,Genetics ,Whole genome sequencing ,Article Subject ,lcsh:QH426-470 ,biology ,Pharmaceutical Science ,Brucellosis ,Brucella ,biology.organism_classification ,medicine.disease ,Biochemistry ,Virology ,Genome ,lcsh:Genetics ,03 medical and health sciences ,030104 developmental biology ,medicine ,Multilocus sequence typing ,Typing ,Molecular Biology ,Prophage ,Research Article ,Brucella melitensis - Abstract
Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year.Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity ofBrucellaspp. in India. We performed multilocus sequence typing of fourB.melitensisstrains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of theB.melitensisisolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis.
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- 2016
15. Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.)
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Reyazul Rouf Mir, R. Varma Penmetsa, Ashutosh Sharma, Kulbhushan Saxena, Rajeev K. Varshney, Himabindu Kudapa, Rachit K. Saxena, Sandhya Srikanth, and Sarwar Azam
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Candidate gene ,Genotype ,Genetic Linkage ,Molecular Sequence Data ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Flowers ,Quantitative trait locus ,Genes, Plant ,Polymorphism, Single Nucleotide ,Cajanus ,Genetics ,Domestication ,Phaseolus ,Comparative genomics ,Comparative Genomic Hybridization ,Original Paper ,Base Sequence ,biology ,Gene Expression Profiling ,Chromosome Mapping ,food and beverages ,General Medicine ,biology.organism_classification ,Phenotype ,Trait ,Soybeans ,Agronomy and Crop Science ,Candidate Gene Analysis ,Biotechnology - Abstract
Key message We report a likely candidate gene, CcTFL1, for determinacy in pigeonpea through candidate gene sequencing analysis, mapping, QTL analysis together with comparative genomics and expression profiling. Abstract Pigeonpea (Cajanus cajan) is the sixth most important legume crop grown on ~5 million hectares globally. Determinacy is an agronomically important trait selected during pigeonpea domestication. In the present study, seven genes related to determinacy/flowering pattern in pigeonpea were isolated through a comparative genomics approach. Single nucleotide polymorphism (SNP) analysis of these candidate genes on 142 pigeonpea lines found a strong association of SNPs with the determinacy trait for three of the genes. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a likely candidate for determinacy in pigeonpea since it explained 45–96 % of phenotypic variation for determinacy, 45 % for flowering time and 77 % for plant height. Comparative genomics analysis of CcTFL1 with the soybean (Glycine max) and common bean (Phaseolus vulgaris) genomes at the micro-syntenic level further enhanced our confidence in CcTFL1 as a likely candidate gene. These findings have been validated by expression analysis that showed down regulation of CcTFL1 in a determinate line in comparison to an indeterminate line. Gene-based markers developed in the present study will allow faster manipulation of the determinacy trait in future breeding programs of pigeonpea and will also help in the development of markers for these traits in other related legume species. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2406-8) contains supplementary material, which is available to authorized users.
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- 2014
16. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
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Mahendar Thudi, Yong Zhang, Frank M. You, Sabhyata Bhatia, Sarwar Azam, Ming-Cheng Luo, Deepa Jaganathan, Oscar Riera-Lizarazu, Reyazul Rouf Mir, Rajeev K. Varshney, Yuqin Hu, and Jinliang Gao
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Genetic Markers ,Chromosomes, Artificial, Bacterial ,Reference genome sequence ,Quantitative Trait Loci ,Biology ,Quantitative trait locus ,Genome ,Contig Mapping ,Chickpea ,Gene mapping ,Stress, Physiological ,Genetics ,Genetic maps ,Genome size ,Disease Resistance ,Plant Diseases ,Whole genome sequencing ,Original Paper ,Bacterial artificial chromosome ,Physical map ,Contig ,food and beverages ,General Medicine ,Physical Chromosome Mapping ,Cicer ,Droughts ,Genome, Plant ,Microsatellite Repeats - Abstract
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement. Electronic supplementary material The online version of this article (doi:10.1007/s10142-014-0363-6) contains supplementary material, which is available to authorized users.
- Published
- 2014
17. Leptospira surface adhesin (Lsa21) induces Toll like receptor 2 and 4 mediated inflammatory responses in macrophages
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Syed M. Faisal, M. Subathra, Vivek Phani Varma, Anil K. Sunkara, Yung-Fu Chang, Mohd Akif, Sarwar Azam, and Mirza S. Baig
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0301 basic medicine ,MAP Kinase Signaling System ,030106 microbiology ,Article ,Cell Line ,Proinflammatory cytokine ,Mice ,03 medical and health sciences ,Leptospira ,Protein Interaction Mapping ,Animals ,Humans ,Leptospirosis ,Phosphorylation ,Adhesins, Bacterial ,Inflammation ,Toll-like receptor ,Multidisciplinary ,Innate immune system ,biology ,Chemistry ,Macrophages ,biology.organism_classification ,Antibodies, Neutralizing ,Immunity, Innate ,Recombinant Proteins ,Toll-Like Receptor 2 ,Cell biology ,Mice, Inbred C57BL ,Toll-Like Receptor 4 ,TLR2 ,HEK293 Cells ,RAW 264.7 Cells ,030104 developmental biology ,Myeloid Differentiation Factor 88 ,Immunology ,TLR4 ,Cytokines ,bacteria ,Female ,Cytokine secretion ,Signal transduction ,Signal Transduction - Abstract
Leptospirosis is zoonotic and emerging infectious disease of global importance. Little is understood about Leptospira pathogenesis and host immune response. In the present work we have investigated how Leptospira modulates the host innate immune response mediated by Toll-like receptors (TLRs) via surface exposed proteins. We screened Leptospira outer membrane/surface proteins for their ability to activate/inhibit TLR2/4 signaling in HEK293 cell lines. Of these the 21 kDa Leptospira surface adhesin, Lsa21 had strong TLR2 and TLR4 activity leading to production of proinflammatory cytokines and expression of costimulatory molecules in mouse macrophages. This activity of Lsa21 on innate response was dependent on activation of mitogen activated protein kinases (MAPKs) via stimulating the rapid phosphorylation of p38, JNK and activation of transcription factor NF-κB. Additionally, neutralizing antibodies against TLR2 and TLR4 significantly inhibited cytokine secretion and attenuated Lsa21 induced phosphorylation of p38 and JNK. Furthermore, Lsa21 induced cytokine levels were significantly lower in TLR2−/− and TLR4−/− than in wild type mouse macrophage cell lines. Confocal microscopy and molecular docking confirmed that Lsa21 interacted with both TLR2 and TLR4. These results indicate that Lsa21 is a potent TLR2 and TLR4 agonist that induces strong innate response and may play important role in Leptospira pathogenesis.
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- 2016
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18. Genome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations
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Hari Parapatla, Sunil Parthasarathy, Sarwar Azam, Ramurthy Gudla, Veera Narasimha Rao, Sujana Ghanta Vemuri, Harshita Yakkala, Annapoorni Lakshman Sagar, and Dayananda Siddavattam
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0301 basic medicine ,030106 microbiology ,Bacterial genome size ,Genome ,biodegradation ,03 medical and health sciences ,Plasmid ,Genetics ,Brevundimonas diminuta ,Selection, Genetic ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Gen Report ,Whole genome sequencing ,biology ,Phylogenetic tree ,aromatic compound degradation ,Sphingomonadales ,Caulobacteraceae ,biology.organism_classification ,Organophosphates ,Sphingomonadaceae ,Sphingopyxis ,biotransformation ,Genome, Bacterial ,Plasmids - Abstract
The complete genome sequence of Brevundimonas diminuta represented a chromosome (∼4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908 and 30,654 bp, respectively. The sequence of the genome showed no significant similarity with the known bacterial genome sequences, instead showed weak similarity with the members of different genera of family, Sphingomonadaceae. Contradicting existing taxonomic position, the core genome-guided phylogenetic tree placed B. diminuta in the genus Sphingopyxis and showed sufficient genome-to-genome distance warranting a new species name. Reflecting the strains ability to grow in harsh environments, the genome-contained genetic repertoire required for mineralization of several recalcitrant man-made aromatic compounds.
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- 2016
19. Identification and Validation of Selected Universal Stress Protein Domain Containing Drought-Responsive Genes in Pigeonpea (Cajanus cajan L.)
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Rachit K. Saxena, L. Krishnamurthy, Vikas K. Singh, Aamir W. Khan, Sarwar Azam, Pallavi Sinha, Lekha T. Pazhamala, and Rajeev K. Varshney
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0106 biological sciences ,0301 basic medicine ,Antiporter ,legumes ,Protein domain ,Drought tolerance ,Plant Science ,Biology ,lcsh:Plant culture ,01 natural sciences ,03 medical and health sciences ,Cajanus ,Genotype ,Gene expression ,in silico analysis ,lcsh:SB1-1110 ,in-silico analysis ,Gene ,Original Research ,Genetics ,business.industry ,pigeonpea ,food and beverages ,biology.organism_classification ,drought responsive genes ,Biotechnology ,Gene expression profiling ,other legumes ,030104 developmental biology ,expression profiling ,business ,010606 plant biology & botany - Abstract
Pigeonpea is a resilient crop, which is relatively more drought tolerant than many other legume crops. To understand the molecular mechanisms of this unique feature of pigeonpea, 51 genes were selected using the Hidden Markov Models (HMM) those codes for proteins having close similarity to universal stress protein domain. Validation of these genes was conducted on three pigeonpea genotypes (ICPL 151, ICPL 8755, and ICPL 227) having different levels of drought tolerance. Gene expression analysis using qRT-PCR revealed 6, 8, and 18 genes to be ≥2-fold differentially expressed in ICPL 151, ICPL 8755, and ICPL 227, respectively. A total of 10 differentially expressed genes showed ≥2-fold up-regulation in the more drought tolerant genotype, which encoded four different classes of proteins. These include plant U-box protein (four genes), universal stress protein A-like protein (four genes), cation/H(+) antiporter protein (one gene) and an uncharacterized protein (one gene). Genes C.cajan_29830 and C.cajan_33874 belonging to uspA, were found significantly expressed in all the three genotypes with ≥2-fold expression variations. Expression profiling of these two genes on the four other legume crops revealed their specific role in pigeonpea. Therefore, these genes seem to be promising candidates for conferring drought tolerance specifically to pigeonpea.
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- 2016
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20. Additional file 26: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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Williams, Angela, Sharma, Mamta, Thatcher, Louise, Sarwar Azam, Hane, James, Sperschneider, Jana, Kidd, Brendan, Anderson, Jonathan, Ghosh, Raju, Gagan Garg, Lichtenzveig, Judith, H. Kistler, Shea, Terrance, Young, Sarah, Sally-Anne Buck, Kamphuis, Lars, Rachit Saxena, Pande, Suresh, Ma, Li-Jun, Varshney, Rajeev, and Singh, Karam
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Primer sequences used for qRT-PCR. (DOCX 12 kb)
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- 2016
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21. Additional file 11: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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Williams, Angela, Sharma, Mamta, Thatcher, Louise, Sarwar Azam, Hane, James, Sperschneider, Jana, Kidd, Brendan, Anderson, Jonathan, Ghosh, Raju, Gagan Garg, Lichtenzveig, Judith, H. Kistler, Shea, Terrance, Young, Sarah, Sally-Anne Buck, Kamphuis, Lars, Rachit Saxena, Pande, Suresh, Ma, Li-Jun, Varshney, Rajeev, and Singh, Karam
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Phylogenetic tree illustrating the relationship between the Fusarium sp. isolates used in this study Branch support values are shown in red. This tree illustrates that the legume-infecting isolates do not appear to be more closely related to each other than to other ff. spp. (PDF 21 kb)
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- 2016
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22. Additional file 4: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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Williams, Angela, Sharma, Mamta, Thatcher, Louise, Sarwar Azam, Hane, James, Sperschneider, Jana, Kidd, Brendan, Anderson, Jonathan, Ghosh, Raju, Gagan Garg, Lichtenzveig, Judith, H. Kistler, Shea, Terrance, Young, Sarah, Sally-Anne Buck, Kamphuis, Lars, Rachit Saxena, Pande, Suresh, Ma, Li-Jun, Varshney, Rajeev, and Singh, Karam
- Abstract
Protein/gene set comparisons across Fusarium sp. (DOCX 11 kb)
- Published
- 2016
- Full Text
- View/download PDF
23. Additional file 3: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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Williams, Angela, Sharma, Mamta, Thatcher, Louise, Sarwar Azam, Hane, James, Sperschneider, Jana, Kidd, Brendan, Anderson, Jonathan, Ghosh, Raju, Gagan Garg, Lichtenzveig, Judith, H. Kistler, Shea, Terrance, Young, Sarah, Sally-Anne Buck, Kamphuis, Lars, Rachit Saxena, Pande, Suresh, Ma, Li-Jun, Varshney, Rajeev, and Singh, Karam
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Sequencing data used for genome assemblies. (DOCX 13 kb)
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- 2016
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24. High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)
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Rashmi Gaur, Sarwar Azam, Debasis Chattopadhyay, Aamir W. Khan, Shalu Choudhary, Gitanjali Yadav, Akhilesh K. Tyagi, Sabhyata Bhatia, Ganga Jeena, and Mukesh K. Jain
- Subjects
Genetic Markers ,Genotyping Techniques ,Genetic Linkage ,Population ,SNP ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,Synteny ,Centimorgan ,chickpea ,Genetics ,education ,Molecular Biology ,Genotyping ,Phylogeny ,Genetic association ,education.field_of_study ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,General Medicine ,Full Papers ,linkage map ,Cicer ,SNP genotyping ,genotyping ,NGS ,Genome, Plant - Abstract
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
- Published
- 2012
25. Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
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Trushar Shah, Gregory D. May, Sarwar Azam, Vivek Thakur, BhanuPrakash Amindala, Jonathan D. G. Jones, Rajeev K. Varshney, Andrew Farmer, David J. Studholme, David Edwards, Jayashree Balaji, and Pradeep Ruperao
- Subjects
Crops, Agricultural ,DNA, Plant ,Genotype ,Sequence analysis ,Single-nucleotide polymorphism ,Plant Science ,Biology ,Polymorphism, Single Nucleotide ,Genome ,DNA sequencing ,Consensus Sequence ,Genetic variation ,Genetics ,SNP ,Ecology, Evolution, Behavior and Systematics ,Molecular breeding ,Base Sequence ,Chromosome Mapping ,Computational Biology ,Genetic Variation ,Reproducibility of Results ,Sequence Analysis, DNA ,Reference Standards ,Cicer ,Transcriptome ,Sequence Alignment ,Genome, Plant ,Reference genome - Abstract
• Premise of the study: Next-generation sequencing (NGS) technologies are frequently used for resequencing and mining of single nucleotide polymorphisms (SNPs) by comparison to a reference genome. In crop species such as chickpea (Cicer arietinum) that lack a reference genome sequence, NGS-based SNP discovery is a challenge. Therefore, unlike probability-based statistical approaches for consensus calling and by comparison with a reference sequence, a coverage-based consensus calling (CbCC) approach was applied and two genotypes were compared for SNP identification. • Methods: A CbCC approach is used in this study with four commonly used short read alignment tools (Maq, Bowtie, Novoalign, and SOAP2) and 15.7 and 22.1 million Illumina reads for chickpea genotypes ICC4958 and ICC1882, together with the chickpea trancriptome assembly (CaTA). • Key results: A nonredundant set of 4543 SNPs was identified between two chickpea genotypes. Experimental validation of 224 randomly selected SNPs showed superiority of Maq among individual tools, as 50.0% of SNPs predicted by Maq were true SNPs. For combinations of two tools, greatest accuracy (55.7%) was reported for Maq and Bowtie, with a combination of Bowtie, Maq, and Novoalign identifying 61.5% true SNPs. SNP prediction accuracy generally increased with increasing reads depth. • Conclusions: This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.
- Published
- 2012
26. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
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Guangyi Fan, Todd P. Michael, R. Varma Penmetsa, Shiaw-Pyng Yang, Reetu Tuteja, Gengyun Zhang, Rajeev K. Varshney, Rachit K. Saxena, Wei Wu, Yupeng Li, Adam M. Whaley, Bicheng Yang, Mark T.A. Donoghue, W. Richard McCombie, Charles Spillane, Jaime Sheridan, Xun Xu, Sarwar Azam, Wenbin Chen, Huanming Yang, Hari D. Upadhyaya, Scott A. Jackson, Kulbhushan Saxena, Andrew Farmer, Jessica A. Schlueter, Arvind K. Bharti, Jun Wang, Trushar Shah, Gregory D. May, Douglas R. Cook, and Aiko Iwata
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Genetic Markers ,Chromosomes, Artificial, Bacterial ,diversification ,Sequence analysis ,Biomedical Engineering ,Bioengineering ,Genes, Plant ,Synteny ,Applied Microbiology and Biotechnology ,Genome ,l ,Cajanus ,Segmental Duplications, Genomic ,genes ,Domestication ,Gene ,database ,Repetitive Sequences, Nucleic Acid ,Segmental duplication ,Whole genome sequencing ,Bacterial artificial chromosome ,biology ,software ,business.industry ,Chromosome Mapping ,Molecular Sequence Annotation ,tool ,Sequence Analysis, DNA ,dynamics ,DNA ,families ,biology.organism_classification ,Biotechnology ,Molecular Medicine ,Soybeans ,program ,business ,Genome, Plant - Abstract
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
- Published
- 2011
27. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
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H. Kistler, James K. Hane, Sarwar Azam, Terrance Shea, Karam B. Singh, Brendan N. Kidd, Sarah Young, Li-Jun Ma, Sally Anne G Buck, Lars G. Kamphuis, Louise F. Thatcher, Judith Lichtenzveig, Suresh Pande, Angela H. Williams, Rachit K. Saxena, Jonathan P. Anderson, Raju Ghosh, Jana Sperschneider, Mamta Sharma, Rajeev K. Varshney, and Gagan Garg
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0301 basic medicine ,Fungal pathogen ,Biology ,Conditionally dispensable chromosomes (CDC) ,Genome ,Host Specificity ,Conserved sequence ,Fungal Proteins ,03 medical and health sciences ,Pathosystem ,Fusarium ,Botany ,Fusarium oxysporum ,Genetics ,Pathogenicity ,DNA, Fungal ,Pulse ,Conserved Sequence ,Phylogeny ,Plant Diseases ,Comparative genomics ,Fungal protein ,Comparative Genomic Hybridization ,Fungal genetics ,food and beverages ,Fabaceae ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,biology.organism_classification ,Effectors ,Medicago truncatula ,Legume ,030104 developmental biology ,Genome, Fungal ,Biotechnology ,Research Article - Abstract
Background Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world’s second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Results Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. Conclusions We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn’t share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2486-8) contains supplementary material, which is available to authorized users.
- Published
- 2015
28. Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses
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Teresa Millán, Sarwar Azam, Weidong Chen, Himabindu Kudapa, Eva Madrid, P. Castro, Josefa Rubio, Juan Gil, Latifeh Ali, Rajeev K. Varshney, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ministry of Higher Education (Syrian Arab Republic), and International Crops Research Institute for the Semi-Arid Tropics
- Subjects
Genetics ,Prostrate ,Candidate gene ,education.field_of_study ,Physical map ,Population ,food and beverages ,Plant Science ,Horticulture ,Biology ,Quantitative trait locus ,Cicer ,RAPD ,Erect ,Genetic marker ,Genetic linkage ,Microsatellite ,Semi-erect ,education ,Indel ,Agronomy and Crop Science ,Linkage analysis - Abstract
A recombinant inbred line population (RIP-9) derived from an interspecific cross (ILC72 × Cr5-10) was evaluated for growth habit during 2 years (2003 and 2004). This RIP was used to develop a pair of near isogenic lines (NILs) for erect vs prostrate growth habit in chickpea. Molecular characterization of the identified pair of NILs was performed using 52 sequence tagged microsatellite site markers distributed over different chickpea linkage groups (CaLG) of the genetic map. It revealed polymorphic markers in CaLG1 and CaLG3. Starting from a previous data base simple linear regression was applied to detect association between markers and growth habit. The RAPD (random amplified polymorphic DNA) marker OPAD091053 mapped on CaLG1 explained the highest percentage (maximum 15.4 %) of the total phenotypic variation for growth habit and it was used to develop a SCAR (sequence characterized amplified region) marker (SCAD091053). New markers were developed from sequences surrounding SCAD091053 in the physical map. QTL (quantitative trait loci) analysis revealed a new QTL (QTLHg2) in CaLG1. The Indel marker (deletion/insertion) Indel 3 and the predicted gene Ca_07000 (14,5 Mb of Ca1) and (15,3 Mb of Ca1) had the highest LOD values explaining 24.6 and 23.4 % of the phenotypic variation in years 2003 and 2004, respectively. To confirm these results, another RIP (RIP-5) derived from an intraspecific cross (WR315 × ILC3279) and segregating for erect vs semi-erect growth habit was employed. RIP-5 allowed mapping the gene (Hg2/hg2) on CaLG1 that was flnaked by two Indel markers (Indel 1 and Indel 2) in the range of 12,3 and 16,2 Mb. So, Hg2/hg2 gene corresponds to QTLHg2 region. The annotated genes Ca_07000 and Ca_06999 were homologues to predicted zinc finger genes in Glycine max and Pisum sativum, respectively. Hence, they could be considered as possible candidate genes., This work has been supported by the project INIA contract RTA2010-00059, co-financed by EU funds (FEDER). Ali L. acknowledges Ph.D. fellowship from Syrian Ministry of High Education and ICRISAT for supporting six months stay at the Center of Excellence in Genomic (ICRISAT, Patancheru, India).
- Published
- 2015
29. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies
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Jun Wang, Jacqueline Batley, Annapurna Chitikineni, Jan Vrána, Rachit K. Saxena, Bunyamin Tar’an, Teresa Millán, Pradeep Ruperao, Chi Song, Jana Čížková, Hana Šimková, Jaroslav Doležel, Pooran M. Gaur, David Edwards, Paul Visendi, Karam B. Singh, Chon-Kit Kenneth Chan, Rajeev K. Varshney, Satomi Hayashi, Miroslava Karafiátová, and Sarwar Azam
- Subjects
Comparative genomics ,Cancer genome sequencing ,Genetics ,Cell Nucleus ,DNA, Plant ,Sequence assembly ,Reproducibility of Results ,Genomics ,Plant Science ,Genome project ,Computational biology ,Sequence Analysis, DNA ,Biology ,Flow Cytometry ,Genome ,Chromosomes, Plant ,Cicer ,Fluorescence ,Genome Size ,Agronomy and Crop Science ,Genome, Plant ,Biotechnology ,Personal genomics ,Reference genome - Abstract
With the expansion of next-generation sequencing technology and advanced bioinformatics, there has been a rapid growth of genome sequencing projects. However, while this technology enables the rapid and cost-effective assembly of draft genomes, the quality of these assemblies usually falls short of gold standard genome assemblies produced using the more traditional BAC by BAC and Sanger sequencing approaches. Assembly validation is often performed by the physical anchoring of genetically mapped markers, but this is prone to errors and the resolution is usually low, especially towards centromeric regions where recombination is limited. New approaches are required to validate reference genome assemblies. The ability to isolate individual chromosomes combined with next-generation sequencing permits the validation of genome assemblies at the chromosome level. We demonstrate this approach by the assessment of the recently published chickpea kabuli and desi genomes. While previous genetic analysis suggests that these genomes should be very similar, a comparison of their chromosome sizes and published assemblies highlights significant differences. Our chromosomal genomics analysis highlights short defined regions that appear to have been misassembled in the kabuli genome and identifies large-scale misassembly in the draft desi genome. The integration of chromosomal genomics tools within genome sequencing projects has the potential to significantly improve the construction and validation of genome assemblies. The approach could be applied both for new genome assemblies as well as published assemblies, and complements currently applied genome assembly strategies.
- Published
- 2013
30. Mapping and identification of a Cicer arietinum NSP2 gene involved in nodulation pathway
- Author
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Teresa Millán, Sarwar Azam, Juan Gil, Rajeev K. Varshney, Latifeh Ali, Josefa Rubio, Eva Madrid, International Crops Research Institute for the Semi-Arid Tropics, Ministry of Higher Education (Syrian Arab Republic), Junta de Andalucía, European Commission, and CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)
- Subjects
Genetics ,Candidate gene ,education.field_of_study ,biology ,Genetic Linkage ,Population ,Mutant ,food and beverages ,General Medicine ,biology.organism_classification ,Genes, Plant ,Medicago truncatula ,Cicer ,Genetic marker ,Genetic linkage ,Nitrogen Fixation ,Botany ,Microsatellite ,education ,Agronomy and Crop Science ,Gene ,Biotechnology ,Plant Proteins - Abstract
An intraspecific cross between the mutant non-nodulating genotype PM233, carrying the recessive gene rn1, and the wild-type CA2139 was used to develop two pairs of near-isogenic lines (NILs) for nodulation in chickpea. These pairs of NILs were characterized using sequence tagged microsatellite site (STMS) markers distributed across different linkage groups (LGs) of the chickpea genetic map leading to the detection of polymorphic markers located in LG5. Using this information, together with the genome annotation in Medicago truncatula, a candidate gene (NSP2) known to be involved in nodulation pathway was selected for mapping in chickpea. The full length sequence obtained in chickpea wild-type (CaNSP2) was 1,503 bp. Linkage analysis in an F3 population of 118 plants derived from the cross between the pair of NILS NIL7-2A (nod) × NIL7-2B (non-nod) revealed a co-localization between CaNSP2 and Rn1 gene. These data implicate the CaNSP2 gene as a candidate for identity to Rn1, and suggest that it could act in the nodulation signaling transduction pathway similarly to that in other legumes species., This work has been supported by the project INIA contract RTA2010-00059, co-financed by EU funds (FEDER). We are also indebted to Dr. F. Temprano (IFAPA, Spain) for his support with Rhizobium inoculations. Ali L acknowledges PhD fellowship from Syrian Ministry of High Education and ICRISAT for supporting 6 months stay at the Center of Excellence in Genomics, ICRISAT, Patancheru, India (http://www.icrisat.org/ceg).
- Published
- 2013
31. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
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Steven B. Cannon, Ying Wang, Xudong Zhang, Chi Song, Janet A. Condie, Shancen Zhao, Benjamin D. Rosen, Noelia Carrasquilla-Garcia, Mahendar Thudi, Chunyan Xu, James K. Hane, Josefa Rubio, Larissa Ramsay, Bunyamin Tar’an, Hari D. Upadhyaya, Narendra Singh, Kailash C. Bansal, Juan Gil, Judith Lichtenzveig, Andrew Farmer, Peter Winter, Gengyun Zhang, Karam B. Singh, Sheng Yu, Rachit K. Saxena, Scott A. Jackson, Jaroslav Dolezel, Sarwar Azam, Andrew G. Sharpe, Carol Soderlund, Xun Xu, David Edwards, Aiko Iwata, Teresa Millán, William Nelson, Swapan K. Datta, Arvind K. Bharti, Rajeev K. Varshney, Ming-Cheng Luo, Krishna K. Gali, Weiming He, C. L. L. Gowda, R. Varma Penmetsa, Guenter Kahl, Pooran M. Gaur, N. Nadarajan, Jun Wang, Douglas R. Cook, and Jong-Min Baek
- Subjects
plant genome ,Genotype ,balancing selection ,Biomedical Engineering ,Bioengineering ,Food supply ,gene sequence ,Biology ,Plant disease resistance ,Applied Microbiology and Biotechnology ,Genome ,Developing countries ,Genetic variation ,chickpea ,Domestication ,Gene ,Phylogeny ,Disease Resistance ,Repetitive Sequences, Nucleic Acid ,Whole genome sequencing ,Molecular breeding ,Shotgun sequencing ,business.industry ,Genetic Variation ,Cicer arietinum ,nucleotide sequence ,Agriculture ,DNA ,Sequence Analysis, DNA ,agronomic trait ,Cicer ,Biotechnology ,Genome sequences ,Trait improvement ,Agronomy ,Genes ,breeding ,Whole-genome shotgun ,Molecular Medicine ,Agronomic traits ,business ,Genome, Plant - Abstract
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea - desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication. Copyright © 2013 Nature America, Inc.
- Published
- 2013
32. Semiotics of Exile in Photography, Intersectional Racism and Epistemic Violence in Natasha Trethewey.
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Zeng, Hong and Sarwar, Azam
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- *
POETRY (Literary form) , *NONFICTION - Published
- 2022
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33. An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
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BhanuPrakash Amindala, Trushar Shah, Sarwar Azam, Rajeev K. Varshney, Mohan A. V. S. K. Katta, Mohan Telluri, Pradeep Ruperao, and Abhishek Rathore
- Subjects
Next-Generation Sequencing ,Computer and Information Sciences ,Java ,Bioinformatics ,lcsh:Medicine ,Genomics ,Plant Science ,Computational biology ,Breeding ,Biology ,Plant Genetics ,Research and Analysis Methods ,Polymorphism, Single Nucleotide ,DNA sequencing ,Computer Architecture ,Software Pipelines ,Database and Informatics Methods ,Plant Genomics ,Genetics ,Data Mining ,lcsh:Science ,Pipelines (Computing) ,Genotyping ,computer.programming_language ,Internet ,Multidisciplinary ,Command-line interface ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Comparative Genomics ,Plants ,Genome Analysis ,Pipeline (software) ,Pipeline transport ,ComputingMethodologies_PATTERNRECOGNITION ,Software-Aided Sequence Analysis ,Plant Biotechnology ,lcsh:Q ,Transcriptome Analysis ,computer ,Genome, Plant ,Software ,Research Article ,Biotechnology ,Reference genome - Abstract
Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.
- Published
- 2014
34. Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications
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Andrew G. Sharpe, Sarwar Azam, Himabindu Kudapa, Benjamin Deonovic, Steven B. Cannon, Rajeev K. Varshney, Connor Cameron, Andrew Farmer, Bunyamin Tar’an, and Rong Li
- Subjects
Sanger sequencing ,plant genome ,Genetic Linkage ,Agricultural Biotechnology ,genotype ,expressed sequence tag ,Plant Science ,Plant Genetics ,Genome ,Transcriptomes ,Transcriptome ,Contig Mapping ,simple sequence repeat ,plant chromosome ,Genome Databases ,Plant Genomics ,Medicago ,genetic polymorphism ,genetic conservation ,Plant Proteins ,next generation sequencing ,Genetics ,Expressed sequence tag ,Multidisciplinary ,Contig ,High-Throughput Nucleotide Sequencing ,food and beverages ,Agriculture ,Genomics ,Plants ,Medicine ,Sequence Analysis ,Research Article ,Biotechnology ,Genetic Markers ,intron ,species comparison ,Sequence analysis ,Science ,Sequence Databases ,Crops ,gene sequence ,Biology ,Genes, Plant ,Phaseolus vulgaris ,Synteny ,contig ,DNA sequencing ,Model Organisms ,Genome Analysis Tools ,Medicago truncatula ,chickpea ,soybean ,Comparative genomics ,Sequence Assembly Tools ,Gene Expression Profiling ,genetic transcription ,Computational Biology ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,Introns ,Cicer ,Plant Biotechnology ,transcriptome ,Developmental Biology ,Microsatellite Repeats - Abstract
A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinum Transcriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/ transcriptomes/cicar/lista-cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
- Published
- 2014
35. Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot' region for drought tolerance in chickpea
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Sandip M. Kale, Pooran M. Gaur, Mahendar Thudi, Sarwar Azam, Deepa Jaganathan, Manish Roorkiwal, Rajeev K. Varshney, Henry T. Nguyen, Tim Sutton, and P. B. Kavi Kishor
- Subjects
Genetic Markers ,Fine mapping ,Genotyping Techniques ,Genetic Linkage ,Population ,Quantitative Trait Loci ,Biology ,Quantitative trait locus ,CAPS/dCAPS ,Genes, Plant ,Polymorphism, Single Nucleotide ,Candidate genes ,Gene mapping ,Chickpea ,Genetic linkage ,Cleaved amplified polymorphic sequence ,Genetics ,education ,Molecular Biology ,Genetic Association Studies ,education.field_of_study ,Original Paper ,Dehydration ,“QTL-hotspot” ,Chromosome Mapping ,food and beverages ,General Medicine ,Drought tolerance ,Marker-assisted breeding ,Cicer ,Genetic distance ,Genetic marker ,Genotyping-by-sequencing - Abstract
To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding. Electronic supplementary material The online version of this article (doi:10.1007/s00438-014-0932-3) contains supplementary material, which is available to authorized users.
- Full Text
- View/download PDF
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