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Pronozin AY, Karetnikov DI, Shmakov NA, Bocharnikova ME, Afonnikova SD, Afonnikov DA, Kolchanov NA. CropGene: a software package for the analysis of genomic and transcriptomic data of agricultural plants. Vavilovskii Zhurnal Genet Selektsii 2025; 29:320-329. [PMID: 40264806 PMCID: PMC12011622 DOI: 10.18699/vjgb-25-35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/15/2025] [Accepted: 01/15/2025] [Indexed: 04/24/2025] Open
Abstract
Currently, the breeding of agricultural plants is increasingly based on the use of molecular biological data on genetic sequences, which makes it possible to significantly accelerate the breeding process, create new plant varieties through genomic editing. These data have a large volume, variety and require a large amount of resources, both labor and computing, to analyze the costs. Data analysis of such volume and complexity can be effective only when using modern bioinformatics methods, which include algorithms for identifying genes, predicting their function, and evaluating the effect of mutation on plant phenotype. Such an analysis has recently become impossible without the use of integrated software systems that solve problems of different levels by executing computational pipelines. The paper describes the CropGene software package developed for the comprehensive analysis of genomic and transcriptomic data of agricultural plants. CropGene includes several blocks of bioinformatic analysis, such as analysis of gene variations, assembly of genomes and transcriptomes, as well as annotation of genes and proteins. CropGene implements new methods for analyzing long non-coding RNAs, protein domains, searching and analyzing polymorphisms, and genome-wide association research. CropGene has a user-friendly interface and supports working with various types of data, which greatly simplifies its use for researchers who do not have deep knowledge in the field of bioinformatics. The paper provides examples of the use of CropGene for the analysis of agricultural organisms such as Solanum tuberosum and Zea mays. With CropGene, genetic markers have been identified that explain up to 50 % of the variability in seed color parameters; potential genes that may become promising material for producing potato varieties; more than 100 thousand new long non-coding RNAs. Orthogroups were also found, the domain structure of which shows a marked similarity with the domain architecture of characteristic secreted A2 phospholipases. Thus, CropGene is an important tool for scientists and practitioners working in the field of agrobiotechnology and plant genetics.
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Affiliation(s)
- A Yu Pronozin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - D I Karetnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N A Shmakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - M E Bocharnikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - S D Afonnikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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Ngoh IA, Mane K, Manneh J, Bojang F, Jawara AS, Akenji TN, Anong DN, D’Alessandro U, Amambua-Ngwa A. Transcriptome analysis reveals molecular targets of erythrocyte invasion phenotype diversity in natural Plasmodium falciparum isolates from Cameroon. FRONTIERS IN PARASITOLOGY 2024; 3:1370615. [PMID: 39817175 PMCID: PMC11731687 DOI: 10.3389/fpara.2024.1370615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/24/2024] [Indexed: 01/18/2025]
Abstract
Further understanding of the molecular mediators of alternative RBC invasion phenotypes in endemic malaria parasites will support malaria blood-stage vaccine or drug development. This study investigated the prevalence of sialic acid (SA)-dependent and SA-independent RBC invasion pathways in endemic Plasmodium falciparum parasites from Cameroon and compared the schizont stage transcriptomes in these two groups to uncover the wider repertoire of transcriptional variation associated with the use of alternative RBC invasion pathway phenotypes. A two-color flow cytometry-based invasion-inhibition assay against RBCs treated with neuraminidase, trypsin, and chymotrypsin and deep RNA sequencing of schizont stages harvested in the first ex vivo replication cycle in culture were employed in this investigation. RBC invasion phenotypes were determined for 63 isolates from asymptomatic children with uncomplicated malaria. Approximately 80% of the isolates invaded neuraminidase-treated but not chymotrypsin-treated RBCs, representing SA-independent pathways of RBC invasion. The schizont transcriptome profiles of 16 isolates with invasion phenotypes revealed a total of 5,136 gene transcripts, with 85% of isolates predicted at schizont stages. Two distinct transcriptome profile clusters belonging to SA-dependent and SA-independent parasites were obtained by data reduction with principal component analysis. Differential analysis of gene expression between the two clusters implicated, in addition to the well-characterized adhesins, the upregulation of genes encoding proteins mediating merozoite organelle discharges as well as several conserved, virulent, merozoite-associated, and exported proteins. The latter majority have been shown to have structural and physiological relevance to RBC surface remodeling and immune evasion in malaria and thus have potential as anti-invasion targets.
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Affiliation(s)
- Ines A. Ngoh
- Department of Microbiology and Parasitology, University of Bamenda, Bambili, Cameroon
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
| | - Karim Mane
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Jarra Manneh
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
| | - Fatoumata Bojang
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
| | - Aminata S. Jawara
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
| | - Theresia N. Akenji
- Department of Microbiology and Parasitology, University of Bamenda, Bambili, Cameroon
| | - Damian N. Anong
- Department of Microbiology and Parasitology, University of Bamenda, Bambili, Cameroon
| | - Umberto D’Alessandro
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination (DCE), Medical Research Council The Gambia Unit at the London School of Hygiene and Tropical Medicine (LSHTM), Fajara, Gambia
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Miller JR, Adjeroh DA. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq. BMC Bioinformatics 2024; 25:109. [PMID: 38475727 DOI: 10.1186/s12859-024-05728-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference. RESULTS We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair. CONCLUSIONS For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.
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Affiliation(s)
- Jason R Miller
- Department of Computer Science, Mathematics, Engineering, Shepherd University, Shepherdstown, WV, USA.
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway.
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
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Fenn A, Tsoy O, Faro T, Rößler FM, Dietrich A, Kersting J, Louadi Z, Lio CT, Völker U, Baumbach J, Kacprowski T, List M. Alternative splicing analysis benchmark with DICAST. NAR Genom Bioinform 2023; 5:lqad044. [PMID: 37260511 PMCID: PMC10227362 DOI: 10.1093/nargab/lqad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/13/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for analysing alternative splicing integrating eleven splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.
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Affiliation(s)
| | | | - Tim Faro
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Fanny L M Rößler
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Alexander Dietrich
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Johannes Kersting
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Zakaria Louadi
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Chit Tong Lio
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5000 Odense, Denmark
| | | | - Markus List
- To whom correspondence should be addressed. Tel: +49 8161 71 2761;
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Gerasimova SV, Kolosovskaya EV, Vikhorev AV, Korotkova AM, Hertig CW, Genaev MA, Domrachev DV, Morozov SV, Chernyak EI, Shmakov NA, Vasiliev GV, Kochetov AV, Kumlehn J, Khlestkina EK. WAX INDUCER 1 Regulates β-Diketone Biosynthesis by Mediating Expression of the Cer-cqu Gene Cluster in Barley. Int J Mol Sci 2023; 24:ijms24076762. [PMID: 37047735 PMCID: PMC10095013 DOI: 10.3390/ijms24076762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Plant surface properties are crucial determinants of resilience to abiotic and biotic stresses. The outer layer of the plant cuticle consists of chemically diverse epicuticular waxes. The WAX INDUCER1/SHINE subfamily of APETALA2/ETHYLENE RESPONSIVE FACTORS regulates cuticle properties in plants. In this study, four barley genes homologous to the Arabidopsis thaliana AtWIN1 gene were mutated using RNA-guided Cas9 endonuclease. Mutations in one of them, the HvWIN1 gene, caused a recessive glossy sheath phenotype associated with β-diketone deficiency. A complementation test for win1 knockout (KO) and cer-x mutants showed that Cer-X and WIN1 are allelic variants of the same genomic locus. A comparison of the transcriptome from leaf sheaths of win1 KO and wild-type plants revealed a specific and strong downregulation of a large gene cluster residing at the previously known Cer-cqu locus. Our findings allowed us to postulate that the WIN1 transcription factor in barley is a master mediator of the β-diketone biosynthesis pathway acting through developmental stage- and organ-specific transactivation of the Cer-cqu gene cluster.
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Affiliation(s)
- Sophia V Gerasimova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | | | - Alexander V Vikhorev
- Vavilov Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Anna M Korotkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Christian W Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Mikhail A Genaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitry V Domrachev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sergey V Morozov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena I Chernyak
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikolay A Shmakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Gennady V Vasiliev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alex V Kochetov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Elena K Khlestkina
- Vavilov Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
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Yamamoto N, Tong W, Lv B, Peng Z, Yang Z. The Original Form of C 4-Photosynthetic Phospho enolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905894. [PMID: 35958195 PMCID: PMC9358456 DOI: 10.3389/fpls.2022.905894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Poaceae is the most prominent monocot family that contains the primary cereal crops wheat, rice, and maize. These cereal species exhibit physiological diversity, such as different photosynthetic systems and environmental stress tolerance. Phosphoenolpyruvate carboxylase (PEPC) in Poaceae is encoded by a small multigene family and plays a central role in C4-photosynthesis and dicarboxylic acid metabolism. Here, to better understand the molecular basis of the cereal species diversity, we analyzed the PEPC gene family in wheat together with other grass species. We could designate seven plant-type and one bacterial-type grass PEPC groups, ppc1a, ppc1b, ppc2a, ppc2b, ppc3, ppc4, ppcC4, and ppc-b, respectively, among which ppc1b is an uncharacterized type of PEPC. Evolutionary inference revealed that these PEPCs were derived from five types of ancient PEPCs (ppc1, ppc2, ppc3, ppc4, and ppc-b) in three chromosomal blocks of the ancestral Poaceae genome. C4-photosynthetic PEPC (ppcC4 ) had evolved from ppc1b, which seemed to be arisen by a chromosomal duplication event. We observed that ppc1b was lost in many Oryza species but preserved in Pooideae after natural selection. In silico analysis of cereal RNA-Seq data highlighted the preferential expression of ppc1b in upper ground organs, selective up-regulation of ppc1b under osmotic stress conditions, and nitrogen response of ppc1b. Characterization of wheat ppc1b showed high levels of gene expression in young leaves, transcriptional responses under nitrogen and abiotic stress, and the presence of a Dof1 binding site, similar to ppcC4 in maize. Our results indicate the evolving status of Poaceae PEPCs and suggest the functional association of ppc1-derivatives with adaptation to environmental changes.
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Affiliation(s)
- Naoki Yamamoto
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Wurina Tong
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Bingbing Lv
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang College, Xichang, China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
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Glagoleva AY, Vikhorev AV, Shmakov NA, Morozov SV, Chernyak EI, Vasiliev GV, Shatskaya NV, Khlestkina EK, Shoeva OY. Features of Activity of the Phenylpropanoid Biosynthesis Pathway in Melanin-Accumulating Barley Grains. FRONTIERS IN PLANT SCIENCE 2022; 13:923717. [PMID: 35898231 PMCID: PMC9310326 DOI: 10.3389/fpls.2022.923717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Barley (Hordeum vulgare L.) grain pigmentation is caused by two types of phenolic compounds: anthocyanins (which are flavonoids) give a blue or purple color, and melanins (which are products of enzymatic oxidation and polymerization of phenolic compounds) give a black or brown color. Genes Ant1 and Ant2 determine the synthesis of purple anthocyanins in the grain pericarp, whereas melanins are formed under the control of the Blp1 gene in hulls and pericarp tissues. Unlike anthocyanin synthesis, melanin synthesis is poorly understood. The objective of the current work was to reveal features of the phenylpropanoid biosynthesis pathway functioning in melanin-accumulating barley grains. For this purpose, comparative transcriptomic and metabolomic analyses of three barley near-isogenic lines accumulating anthocyanins, melanins, or both in the grain, were performed. A comparative analysis of mRNA libraries constructed for three stages of spike development (booting, late milk, and early dough) showed transcriptional activation of genes encoding enzymes of the general phenylpropanoid pathway in all the lines regardless of pigmentation; however, as the spike matured, unique transcriptomic patterns associated with melanin and anthocyanin synthesis stood out. Secondary activation of transcription of the genes encoding enzymes of the general phenylpropanoid pathway together with genes of monolignol synthesis was revealed in the line accumulating only melanin. This pattern differs from the one observed in the anthocyanin-accumulating lines, where - together with the genes of general phenylpropanoid and monolignol synthesis pathways - flavonoid biosynthesis genes were found to be upregulated, with earlier activation of these genes in the line accumulating both types of pigments. These transcriptomic shifts may underlie the observed differences in concentrations of phenylpropanoid metabolites analyzed in the grain at a late developmental stage by high-performance liquid chromatography. Both melanin-accumulating lines showed an increased total level of benzoic acids. By contrast, anthocyanin-accumulating lines showed higher concentrations of flavonoids and p-coumaric and ferulic acids. A possible negative effect of melanogenesis on the total flavonoid content and a positive influence on the anthocyanin content were noted in the line accumulating both types of pigments. As a conclusion, redirection of metabolic fluxes in the phenylpropanoid biosynthesis pathway occurs when melanin is synthesized.
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Affiliation(s)
- Anastasiia Y. Glagoleva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, ICG, SB RAS, Novosibirsk, Russia
| | - Alexander V. Vikhorev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolay A. Shmakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, ICG, SB RAS, Novosibirsk, Russia
| | - Sergey V. Morozov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, Novosibirsk, Russia
| | - Elena I. Chernyak
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, Novosibirsk, Russia
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, ICG, SB RAS, Novosibirsk, Russia
| | - Natalia V. Shatskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, ICG, SB RAS, Novosibirsk, Russia
| | - Elena K. Khlestkina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources, Saint Petersburg, Russia
| | - Olesya Y. Shoeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, ICG, SB RAS, Novosibirsk, Russia
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8
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Approaches in Gene Coexpression Analysis in Eukaryotes. BIOLOGY 2022; 11:biology11071019. [PMID: 36101400 PMCID: PMC9312353 DOI: 10.3390/biology11071019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. Coexpressed genes are clustered in smaller subnetworks, the predominant biological roles of which can be determined through enrichment analysis. By studying well-annotated gene partners, the attribution of new roles to genes of unknown function or assumption for participation in common metabolic pathways can be achieved, through a guilt-by-association approach. In this review, we present key issues in gene coexpression analysis, as well as the most popular tools that perform it. Abstract Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied extensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensible account of the steps required for performing a complete gene coexpression analysis in eukaryotic organisms. We comment on the use of RNA-Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.
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9
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Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Technology dictates algorithms: recent developments in read alignment. Genome Biol 2021; 22:249. [PMID: 34446078 PMCID: PMC8390189 DOI: 10.1186/s13059-021-02443-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.
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Affiliation(s)
- Mohammed Alser
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Jeremy Rotman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Dhrithi Deshpande
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Kodi Taraszka
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Huwenbo Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pelin Icer Baykal
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Harry Taegyun Yang
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Ph.D. Program, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Victor Xue
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Brunilda Balliu
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - David Koslicki
- Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16801, USA
- Biology Department, Pennsylvania State University, University Park, PA, 16801, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16801, USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Can Alkan
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Bilkent-Hacettepe Health Sciences and Technologies Program, Ankara, Turkey
| | - Onur Mutlu
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA.
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Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. Proc Natl Acad Sci U S A 2019; 116:17121-17126. [PMID: 31399544 PMCID: PMC6708379 DOI: 10.1073/pnas.1822046116] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Understanding the mechanisms of vaccine-elicited protection contributes to the development of new vaccines. The emerging field of systems vaccinology provides detailed information on host responses to vaccination and has been successfully applied to study the molecular mechanisms of several vaccines. Long noncoding RNAs (lncRNAs) are crucially involved in multiple biological processes, but their role in vaccine-induced immunity has not been explored. We performed an analysis of over 2,000 blood transcriptome samples from 17 vaccine cohorts to identify lncRNAs potentially involved with antibody responses to influenza and yellow fever vaccines. We have created an online database where all results from this analysis can be accessed easily. We found that lncRNAs participate in distinct immunological pathways related to vaccine-elicited responses. Among them, we showed that the expression of lncRNA FAM30A was high in B cells and correlates with the expression of immunoglobulin genes located in its genomic vicinity. We also identified altered expression of these lncRNAs in RNA-sequencing (RNA-seq) data from a cohort of children following immunization with intranasal live attenuated influenza vaccine, suggesting a common role across several diverse vaccines. Taken together, these findings provide evidence that lncRNAs have a significant impact on immune responses induced by vaccination.
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11
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Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021255] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene expression is the fundamental level at which the results of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing (RNA-seq) provides a quantitative and open system for profiling transcriptional outcomes on a large scale and therefore facilitates a large diversity of applications, including basic science studies, but also agricultural or clinical situations. In the past 10 years or so, much has been learned about the characteristics of the RNA-seq data sets, as well as the performance of the myriad of methods developed. In this review, we give an overview of the developments in RNA-seq data analysis, including experimental design, with an explicit focus on the quantification of gene expression and statistical approachesfor differential expression. We also highlight emerging data types, such as single-cell RNA-seq and gene expression profiling using long-read technologies.
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Affiliation(s)
- Koen Van den Berge
- Bioinformatics Institute Ghent and Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Katharina M. Hembach
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Charlotte Soneson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Simone Tiberi
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Lieven Clement
- Bioinformatics Institute Ghent and Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Michael I. Love
- Department of Biostatistics and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Rob Patro
- Department of Computer Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Mark D. Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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12
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Gurunathan S, Qasim M, Park C, Yoo H, Choi DY, Song H, Park C, Kim JH, Hong K. Cytotoxicity and Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells. Int J Mol Sci 2018; 19:ijms19113618. [PMID: 30453526 PMCID: PMC6275036 DOI: 10.3390/ijms19113618] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022] Open
Abstract
The rapid development of nanotechnology has led to the use of silver nanoparticles (AgNPs) in biomedical applications, including antibacterial, antiviral, anti-inflammatory, and anticancer therapies. The molecular mechanism of AgNPs-induced cytotoxicity has not been studied thoroughly using a combination of cellular assays and RNA sequencing (RNA-Seq) analysis. In this study, we prepared AgNPs using myricetin, an anti-oxidant polyphenol, and studied their effects on NIH3T3 mouse embryonic fibroblasts as an in vitro model system to explore the potential biomedical applications of AgNPs. AgNPs induced loss of cell viability and cell proliferation in a dose-dependent manner, as evident by increased leakage of lactate dehydrogenase (LDH) from cells. Reactive oxygen species (ROS) were a potential source of cytotoxicity. AgNPs also incrementally increased oxidative stress and the level of malondialdehyde, depleted glutathione and superoxide dismutase, reduced mitochondrial membrane potential and adenosine triphosphate (ATP), and caused DNA damage by increasing the level of 8-hydroxy-2′-deoxyguanosine and the expressions of the p53 and p21 genes in NIH3T3 cells. Thus, activation of oxidative stress may be crucial for NIH3T3 cytotoxicity. Interestingly, gene ontology (GO) term analysis revealed alterations in epigenetics-related biological processes including nucleosome assembly and DNA methylation due to AgNPs exposure. This study is the first demonstration that AgNPs can alter bulk histone gene expression. Therefore, our genome-scale study suggests that the apoptosis observed in NIH3T3 cells treated with AgNPs is mediated by the repression of genes required for cell survival and the aberrant enhancement of nucleosome assembly components to induce apoptosis.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Dong Yoon Choi
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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