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Penin AA, Kasianov AS, Klepikova AV, Omelchenko DO, Makarenko MS, Logacheva MD. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 2024; 22:52. [PMID: 38439107 PMCID: PMC10913212 DOI: 10.1186/s12915-024-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. RESULTS We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance-both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. CONCLUSIONS C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
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Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - Artem S Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Krinitsina AA, Omelchenko DO, Kasianov AS, Karaseva VS, Selezneva YM, Chesnokova OV, Shirobokov VA, Polevova SV, Severova EE. Aerobiological Monitoring and Metabarcoding of Grass Pollen. Plants (Basel) 2023; 12:2351. [PMID: 37375978 DOI: 10.3390/plants12122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
Grass pollen is one of the leading causes of pollinosis, affecting 10-30% of the world's population. The allergenicity of pollen from different Poaceae species is not the same and is estimated from moderate to high. Aerobiological monitoring is a standard method that allows one to track and predict the dynamics of allergen concentration in the air. Poaceae is a stenopalynous family, and thus grass pollen can usually be identified only at the family level with optical microscopy. Molecular methods, in particular the DNA barcoding technique, can be used to conduct a more accurate analysis of aerobiological samples containing the DNA of various plant species. This study aimed to test the possibility of using the ITS1 and ITS2 nuclear loci for determining the presence of grass pollen from air samples via metabarcoding and to compare the analysis results with the results of phenological observations. Based on the high-throughput sequencing data, we analyzed the changes in the composition of aerobiological samples taken in the Moscow and Ryazan regions for three years during the period of active flowering of grasses. Ten genera of the Poaceae family were detected in airborne pollen samples. The representation for most of them for ITS1 and ITS2 barcodes was similar. At the same time, in some samples, the presence of specific genera was characterized by only one sequence: either ITS1 or ITS2. Based on the analysis of the abundance of both barcode reads in the samples, the following order could describe the change with time in the dominant species in the air: Poa, Alopecurus, and Arrhenatherum in early mid-June, Lolium, Bromus, Dactylis, and Briza in mid-late June, Phleum, Elymus in late June to early July, and Calamagrostis in early mid-July. In most samples, the number of taxa found via metabarcoding analysis was higher compared to that in the phenological observations. The semi-quantitative analysis of high-throughput sequencing data well reflects the abundance of only major grass species at the flowering stage.
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Affiliation(s)
- Anastasia A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Artem S Kasianov
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Vera S Karaseva
- Department of Biology, Institute of Natural Science, S.A. Esenin Ryazan State University, 390000 Ryazan, Russia
| | - Yulia M Selezneva
- Department of Biology, Institute of Natural Science, S.A. Esenin Ryazan State University, 390000 Ryazan, Russia
| | - Olga V Chesnokova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vitaly A Shirobokov
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Svetlana V Polevova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena E Severova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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3
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Subkhankulova T, Camargo Sosa K, Uroshlev LA, Nikaido M, Shriever N, Kasianov AS, Yang X, Rodrigues FSLM, Carney TJ, Bavister G, Schwetlick H, Dawes JHP, Rocco A, Makeev VJ, Kelsh RN. Zebrafish pigment cells develop directly from persistent highly multipotent progenitors. Nat Commun 2023; 14:1258. [PMID: 36878908 PMCID: PMC9988989 DOI: 10.1038/s41467-023-36876-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Neural crest cells are highly multipotent stem cells, but it remains unclear how their fate restriction to specific fates occurs. The direct fate restriction model hypothesises that migrating cells maintain full multipotency, whilst progressive fate restriction envisages fully multipotent cells transitioning to partially-restricted intermediates before committing to individual fates. Using zebrafish pigment cell development as a model, we show applying NanoString hybridization single cell transcriptional profiling and RNAscope in situ hybridization that neural crest cells retain broad multipotency throughout migration and even in post-migratory cells in vivo, with no evidence for partially-restricted intermediates. We find that leukocyte tyrosine kinase early expression marks a multipotent stage, with signalling driving iridophore differentiation through repression of fate-specific transcription factors for other fates. We reconcile the direct and progressive fate restriction models by proposing that pigment cell development occurs directly, but dynamically, from a highly multipotent state, consistent with our recently-proposed Cyclical Fate Restriction model.
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Affiliation(s)
| | - Karen Camargo Sosa
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Leonid A Uroshlev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
| | - Masataka Nikaido
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo Pref., 678-1297, Japan
| | - Noah Shriever
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- A.A. Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia
| | - Xueyan Yang
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- The MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | | | - Thomas J Carney
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Lee Kong Chian School of Medicine, Experimental Medicine Building, Yunnan Garden Campus, Nanyang Technological University, 59 Nanyang Drive, Yunnan Garden, 636921, Singapore
| | - Gemma Bavister
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hartmut Schwetlick
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Jonathan H P Dawes
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Andrea Rocco
- Department of Microbial Sciences, FHMS, University of Surrey, GU2 7XH, Guildford, UK
- Department of Physics, FEPS, University of Surrey, GU2 7XH, Guildford, UK
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- Laboratory 'Regulatory Genomics', Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia
| | - Robert N Kelsh
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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5
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Klepikova AV, Kasianov AS, Ezhova MA, Penin AA, Logacheva MD. Transcriptome atlas of Phalaenopsis equestris. PeerJ 2021; 9:e12600. [PMID: 34966594 PMCID: PMC8667740 DOI: 10.7717/peerj.12600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 11/15/2021] [Indexed: 11/27/2022] Open
Abstract
The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.
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Affiliation(s)
- Anna V Klepikova
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S Kasianov
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Margarita A Ezhova
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Maria D Logacheva
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
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6
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Slezina MP, Istomina EA, Korostyleva TV, Kovtun AS, Kasianov AS, Konopkin AA, Shcherbakova LA, Odintsova TI. Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Fusarium oxysporum Infection in Tomato Based on Transcriptome Profiling. Int J Mol Sci 2021; 22:ijms22115741. [PMID: 34072144 PMCID: PMC8198727 DOI: 10.3390/ijms22115741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022] Open
Abstract
Cysteine-rich peptides (CRPs) play an important role in plant physiology. However, their role in resistance induced by biogenic elicitors remains poorly understood. Using whole-genome transcriptome sequencing and our CRP search algorithm, we analyzed the repertoire of CRPs in tomato Solanum lycopersicum L. in response to Fusarium oxysporum infection and elicitors from F. sambucinum. We revealed 106 putative CRP transcripts belonging to different families of antimicrobial peptides (AMPs), signaling peptides (RALFs), and peptides with non-defense functions (Major pollen allergen of Olea europaea (Ole e 1 and 6), Maternally Expressed Gene (MEG), Epidermal Patterning Factor (EPF)), as well as pathogenesis-related proteins of families 1 and 4 (PR-1 and 4). We discovered a novel type of 10-Cys-containing hevein-like AMPs named SlHev1, which was up-regulated both by infection and elicitors. Transcript profiling showed that F. oxysporum infection and F. sambucinum elicitors changed the expression levels of different overlapping sets of CRP genes, suggesting the diversification of functions in CRP families. We showed that non-specific lipid transfer proteins (nsLTPs) and snakins mostly contribute to the response of tomato plants to the infection and the elicitors. The involvement of CRPs with non-defense function in stress reactions was also demonstrated. The results obtained shed light on the mode of action of F. sambucinum elicitors and the role of CRP families in the immune response in tomato.
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Affiliation(s)
- Marina P. Slezina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Ekaterina A. Istomina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Tatyana V. Korostyleva
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Alexey S. Kovtun
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia;
| | - Artem S. Kasianov
- Laboratory of Plant Genomics, Institute for Information Transmission Problems RAS, 127051 Moscow, Russia;
| | - Alexey A. Konopkin
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Larisa A. Shcherbakova
- Laboratory of Physiological Plant Pathology, All-Russian Research Institute of Phytopathology, B. Vyazyomy, 143050 Moscow, Russia;
| | - Tatyana I. Odintsova
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
- Correspondence:
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7
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Bezmenova AV, Zvyagina EA, Fedotova AV, Kasianov AS, Neretina TV, Penin AA, Bazykin GA, Kondrashov AS. Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune. Mol Biol Evol 2021; 37:2279-2286. [PMID: 32243532 PMCID: PMC7403608 DOI: 10.1093/molbev/msaa083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The basidiomycete Schizophyllum commune has the highest level of genetic polymorphism known among living organisms. In a previous study, it was also found to have a moderately high per-generation mutation rate of 2×10−8, likely contributing to its high polymorphism. However, this rate has been measured only in an experiment on Petri dishes, and it is unclear how it translates to natural populations. Here, we used an experimental design that measures the rate of accumulation of de novo mutations in a linearly growing mycelium. We show that S. commune accumulates mutations at a rate of 1.24×10−7 substitutions per nucleotide per meter of growth, or ∼2.04×10−11 per nucleotide per cell division. In contrast to what has been observed in a number of species with extensive vegetative growth, this rate does not decline in the course of propagation of a mycelium. As a result, even a moderate per-cell-division mutation rate in S. commune can translate into a very high per-generation mutation rate when the number of cell divisions between consecutive meiosis is large.
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Affiliation(s)
| | | | - Anna V Fedotova
- Center of Life Sciences, Skoltech, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S Kasianov
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | - Tatiana V Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,N. A. Pertsov White Sea Biological Station, Lomonosov Moscow State University, Primorskiy, Russia
| | - Aleksey A Penin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Georgii A Bazykin
- Center of Life Sciences, Skoltech, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Alexey S Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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8
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Klepikova AV, Shnayder ED, Kasianov AS, Remizowa MV, Sokoloff DD, Penin AA. lepidium-like, a Naturally Occurring Mutant of Capsella bursa-pastoris, and Its Implications on the Evolution of Petal Loss in Cruciferae. Front Plant Sci 2021; 12:714711. [PMID: 34899769 PMCID: PMC8656458 DOI: 10.3389/fpls.2021.714711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/20/2021] [Indexed: 05/06/2023]
Abstract
Naturally occurring mutants whose phenotype recapitulates the changes that distinguish closely related species are of special interest from the evolutionary point of view. They can give a key about the genetic control of the changes that led to speciation. In this study, we described lepidium-like (lel), a naturally occurring variety of an allotetraploid species Capsella bursa-pastoris that is characterized by the typical loss of all four petals. In some cases, one or two basal flowers in the raceme had one or two small petals. The number and structure of other floral organs are not affected. Our study of flower development in the mutant showed that once initiated, petals either cease further development and cannot be traced in anthetic flowers or sometimes develop to various degrees. lel plants showed an earlier beginning of floral organ initiation and delayed petal initiation compared to the wild-type plants. lel phenotype has a wide geographical distribution, being found at the northern extremity of the species range as well as in the central part. The genetic analysis of inheritance demonstrated that lel phenotype is controlled by two independent loci. While the flower in the family Cruciferae generally has a very stable structure (i.e., four sepals, four petals, six stamens, and two carpels), several deviations from this ground plan are known, in particular in the genus Lepidium, C. bursa-pastoris is an emerging model for the study of polyploidy (which is also very widespread in Cruciferae); the identification and characterization of the apetalous mutant lays a foundation for further research of morphological evolution in polyploids.
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Affiliation(s)
- Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Elina D. Shnayder
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Aleksey A. Penin,
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9
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Penin AA, Kasianov AS, Klepikova AV, Kirov IV, Gerasimov ES, Fesenko AN, Logacheva MD. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. Front Plant Sci 2021; 12:612382. [PMID: 33815435 PMCID: PMC8010679 DOI: 10.3389/fpls.2021.612382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
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Affiliation(s)
- Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Maria D. Logacheva,
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10
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Veselovsky VA, Dyachkova MS, Menyaylo EA, Polyaeva PS, Olekhnovich EI, Shitikov EA, Bespiatykh DA, Semashko TA, Kasianov AS, Ilina EN, Danilenko VN, Klimina KM. Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors. Front Immunol 2020; 11:595877. [PMID: 33304352 PMCID: PMC7701253 DOI: 10.3389/fimmu.2020.595877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro. By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance.
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Affiliation(s)
- Vladimir A Veselovsky
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Marina S Dyachkova
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Egor A Menyaylo
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Polina S Polyaeva
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Evgenii I Olekhnovich
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Egor A Shitikov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry A Bespiatykh
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Artem S Kasianov
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia.,Laboratory of Plant Genomics, The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valeriy N Danilenko
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ksenia M Klimina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
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11
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Valyaeva AA, Zharikova AA, Kasianov AS, Vassetzky YS, Sheval EV. Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19. Sci Rep 2020; 10:17772. [PMID: 33082395 PMCID: PMC7576138 DOI: 10.1038/s41598-020-74598-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023] Open
Abstract
SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anastasia A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991
- The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia, 127051
| | - Artem S Kasianov
- The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia, 127051
| | - Yegor S Vassetzky
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France.
- Koltzov Institute of Developmental Biology, Moscow, Russia, 117334.
| | - Eugene V Sheval
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991.
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991.
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12
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Klimina KM, Voroshilova VN, Poluektova EU, Veselovsky VA, Yunes RA, Kovtun AS, Kudryavtseva AV, Kasianov AS, Danilenko VN. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins (Basel) 2020; 12:toxins12060388. [PMID: 32545455 PMCID: PMC7354421 DOI: 10.3390/toxins12060388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023] Open
Abstract
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.
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Affiliation(s)
- Ksenia M. Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
- Correspondence:
| | - Viktoriya N. Voroshilova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Vladimir A. Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Roman A. Yunes
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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13
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Logacheva MD, Schelkunov MI, Fesenko AN, Kasianov AS, Penin AA. Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat. Plants (Basel) 2020; 9:E618. [PMID: 32408719 PMCID: PMC7285332 DOI: 10.3390/plants9050618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022]
Abstract
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.
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Affiliation(s)
- Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksey N. Fesenko
- Federal Scientific Center of Legumes and Groat Crops, 302502 Orel, Russia;
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
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14
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Babenko VV, Podgorny OV, Manuvera VA, Kasianov AS, Manolov AI, Grafskaia EN, Shirokov DA, Kurdyumov AS, Vinogradov DV, Nikitina AS, Kovalchuk SI, Anikanov NA, Butenko IO, Pobeguts OV, Matyushkina DS, Rakitina DV, Kostryukova ES, Zgoda VG, Baskova IP, Trukhan VM, Gelfand MS, Govorun VM, Schiöth HB, Lazarev VN. Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches. BMC Genomics 2020; 21:331. [PMID: 32349672 PMCID: PMC7191736 DOI: 10.1186/s12864-020-6748-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today. RESULTS We annotated the Hirudo medicinalis genome and performed RNA-seq on salivary cells isolated from three closely related leech species, H. medicinalis, Hirudo orientalis, and Hirudo verbana. Differential expression analysis verified by proteomics identified salivary cell-specific gene expression, many of which encode previously unknown salivary components. However, the genes encoding known anticoagulants have been found to be expressed not only in salivary cells. The function-related analysis of the unique salivary cell genes enabled an update of the concept of interactions between salivary proteins and components of haemostasis. CONCLUSIONS Here we report a genome draft of Hirudo medicinalis and describe identification of novel salivary proteins and new homologs of genes encoding known anticoagulants in transcriptomes of three medicinal leech species. Our data provide new insights in genetics of blood-feeding lifestyle in leeches.
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Affiliation(s)
- Vladislav V Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia.
| | - Oleg V Podgorny
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov str, Moscow, 119334, Russia
| | - Valentin A Manuvera
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| | - Artem S Kasianov
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119991, Russia
| | - Alexander I Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Ekaterina N Grafskaia
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| | - Dmitriy A Shirokov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Alexey S Kurdyumov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Dmitriy V Vinogradov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19 Bol'shoi Karetnyi per, Moscow, 127051, Russia
- Skolkovo Institute of Science and Technology, 3 Nobelya Ulitsa str, Moscow, 121205, Russia
| | - Anastasia S Nikitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| | - Sergey I Kovalchuk
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str, Moscow, 117997, Russia
| | - Nickolay A Anikanov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str, Moscow, 117997, Russia
| | - Ivan O Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Olga V Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Daria S Matyushkina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Daria V Rakitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
| | - Victor G Zgoda
- V.N. Orekhovich Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaja str, Moscow, 119832, Russia
| | - Isolda P Baskova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119991, Russia
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University of the Ministry of Healthcare of the Russian Federation (Sechenovskiy University), Trubetskaya str., 8-2, Moscow, 119991, Russia
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19 Bol'shoi Karetnyi per, Moscow, 127051, Russia
- Skolkovo Institute of Science and Technology, 3 Nobelya Ulitsa str, Moscow, 121205, Russia
- Faculty of Computer Science, National Research University Higher School of Economics, 20 Myasnitskaya str, Moscow, 101000, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73 Leninskie Gory, Moscow, 119991, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| | - Helgi B Schiöth
- I.M. Sechenov First Moscow State Medical University of the Ministry of Healthcare of the Russian Federation (Sechenovskiy University), Trubetskaya str., 8-2, Moscow, 119991, Russia
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Husargatan 3, Uppsala, 75124, Sweden
| | - Vassili N Lazarev
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
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Omelchenko DO, Makarenko MS, Kasianov AS, Schelkunov MI, Logacheva MD, Penin AA. Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris. Plants (Basel) 2020; 9:E469. [PMID: 32276324 PMCID: PMC7238199 DOI: 10.3390/plants9040469] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/24/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022]
Abstract
Shepherd's purse (Capsella bursa-pastoris) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in A. thaliana.
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Affiliation(s)
- Denis O. Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Maxim S. Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
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16
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Klimina KM, Batotsyrenova EG, Yunes RA, Gilyaeva EH, Poluektova EU, Kostrova TA, Kudryavtseva AV, Odorskaya MV, Kashuro VA, Kasianov AS, Ivanov MB, Danilenko VN. The effects of desynchronosis on the gut microbiota composition and physiological parameters of rats. BMC Microbiol 2019; 19:160. [PMID: 31299889 PMCID: PMC6626387 DOI: 10.1186/s12866-019-1535-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Background All living organisms experience physiological changes regulated by endogenous circadian rhythms. The main factor controlling the circadian clock is the duration of daylight. The aim of this research was to identify the impact of various lighting conditions on physiological parameters and gut microbiota composition in rats. 3 groups of outbred rats were subjected to normal light-dark cycles, darkness and constant lighting. Results After 1 and 3 months we studied urinary catecholamine levels in rats; indicators of lipid peroxidation and antioxidant activity in the blood; protein levels of BMAL1, CLOCK and THRA in the hypothalamus; composition and functional activity of the gut microbiota. Subjecting the rats to conditions promoting desynchronosis for 3 months caused disruptions in homeostasis. Conclusions Changing the lighting conditions led to changes in almost all the physiological parameters that we studied. Catecholamines can be regarded as a synchronization super system of split-level circadian oscillators. We established a correlation between hypothalamic levels of Bmal1 and urinary catecholamine concentrations. The magnitude of changes in the GM taxonomic composition was different for LL/LD and DD/LD but the direction of these changes was similar. As for the predicted functional properties of the GM which characterize its metabolic activity, they didn’t change as dramatically as the taxonomic composition. All differences may be viewed as a compensatory reaction to new environmental conditions and the organism has adapted to those conditions. Electronic supplementary material The online version of this article (10.1186/s12866-019-1535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ksenia M Klimina
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia. .,Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
| | - Ekaterina G Batotsyrenova
- The Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology Federal Medical Biological Agency of Russia, Saint Petersburg, 192019, Russia
| | - Roman A Yunes
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elena H Gilyaeva
- The Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology Federal Medical Biological Agency of Russia, Saint Petersburg, 192019, Russia
| | - Elena U Poluektova
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Taisia A Kostrova
- The Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology Federal Medical Biological Agency of Russia, Saint Petersburg, 192019, Russia
| | - Anna V Kudryavtseva
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Maya V Odorskaya
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vadim A Kashuro
- The Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology Federal Medical Biological Agency of Russia, Saint Petersburg, 192019, Russia
| | - Artem S Kasianov
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Maksim B Ivanov
- The Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology Federal Medical Biological Agency of Russia, Saint Petersburg, 192019, Russia
| | - Valery N Danilenko
- Department of Genetics and Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
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17
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Klimina KM, Kasianov AS, Poluektova EU, Emelyanov KV, Voroshilova VN, Zakharevich NV, Kudryavtseva AV, Makeev VJ, Danilenko VN. Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes. PeerJ 2019; 7:e6554. [PMID: 30863681 PMCID: PMC6404652 DOI: 10.7717/peerj.6554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/02/2019] [Indexed: 01/22/2023] Open
Abstract
Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
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Affiliation(s)
- Ksenia M Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Artem S Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elena U Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | | | | | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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18
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Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA. An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. BMC Plant Biol 2019; 19:49. [PMID: 30813912 PMCID: PMC6393959 DOI: 10.1186/s12870-019-1636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .
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Affiliation(s)
- Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
| | - Ivan V. Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, Moscow Region, 142290 Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
- Skolkovo Institute of Science and Technology, Nobelya Ulitsa 3, Moscow, 121205 Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
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19
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Penin AA, Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD. Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum. Genes (Basel) 2019; 10:genes10010050. [PMID: 30650673 PMCID: PMC6356586 DOI: 10.3390/genes10010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/04/2018] [Indexed: 11/26/2022] Open
Abstract
The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.
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Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
| | - Artem S Kasianov
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, 119991 Moscow, Russia.
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
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20
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Odintsova TI, Slezina MP, Istomina EA, Korostyleva TV, Kasianov AS, Kovtun AS, Makeev VJ, Shcherbakova LA, Kudryavtsev AM. Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PeerJ 2019; 7:e6125. [PMID: 30643692 PMCID: PMC6329339 DOI: 10.7717/peerj.6125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/18/2018] [Indexed: 01/15/2023] Open
Abstract
Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. These DEFLs, in concert with other defense molecules, are suggested to determine enhanced resistance of elicitor-pretreated wheat seedlings. In addition to providing a better understanding of the mode of action of the elicitors from FS-94 in controlling diseases, up-regulated IR-specific DEFL genes represent novel candidates for genetic transformation of plants and development of pathogen-resistant crops.
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Affiliation(s)
- Tatyana I Odintsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marina P Slezina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Istomina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kovtun
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Larisa A Shcherbakova
- All-Russian Research Institute of Phytopathology, B. Vyazyomy, Moscow Region, Russia
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21
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Novikov AD, Lavrov KV, Kasianov AS, Gerasimova TV, Yanenko AS. Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles. Genome Announc 2018; 6:e01526-17. [PMID: 29439044 PMCID: PMC5805882 DOI: 10.1128/genomea.01526-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
Rhodococcus sp. strain M8 is a nitrile-degrading bacterium isolated from acrylonitrile-contaminated sites. This strain produces the enzymes for sequential nitrile degradation, cobalt-type nitrile hydratase, and amidase in large amounts. Its draft genome sequence, announced here, has an estimated size of 6.3 Mbp.
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Affiliation(s)
- Andrey D Novikov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Konstantin V Lavrov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | | | - Tatyana V Gerasimova
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Alexander S Yanenko
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
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22
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Shtratnikova VY, Belalov I, Kasianov AS, Schelkunov MI, Logacheva Maria DA, Novikov AD, Shatalov AA, Gerasimova TV, Yanenko AS, Makeev VJ. The complete genome of the oil emulsifying strain Thalassolituus oleivorans K-188 from the Barents Sea. Mar Genomics 2018; 37:18-20. [PMID: 33250120 DOI: 10.1016/j.margen.2017.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022]
Abstract
Gammaproteobacterium Thalassolituus oleivorans plays an important role in oil degradation in sea water through emulsifying crude oil and alkanes at low temperatures in polar sea environment. Here we report the complete genome sequence of K-188 strain (VKPM B-9394) isolated in the Barents Sea and compare it with other known Thalassolituus oleivorans strains. The Thalassolituus strains are differed in orthologs number of the genes of alkane degradation, transport proteins, genes of sugar utilization, endonucleases, signaling proteins, transcriptional regulators and presence of CRISPR/Cas locus. Also only the genome of K-188 contains the 3-hydroxyalkanoate synthetase.
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Affiliation(s)
- Victoria Yu Shtratnikova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation.
| | - Ilya Belalov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., h. 33, b. 2, Moscow 119071, Russian Federation.
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Gubkina str., h. 3, Moscow 119991, Russian Federation.
| | - Mikhail I Schelkunov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation; Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow 127051, Russian Federation.
| | - D A Logacheva Maria
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, h. 1, b. 40, Moscow 119991, Russian Federation.
| | - Andrey D Novikov
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Alexey A Shatalov
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Tatyana V Gerasimova
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation
| | - Alexander S Yanenko
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation.
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Gubkina str., h. 3, Moscow 119991, Russian Federation; State Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., h. 1, Moscow 117545, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russian Federation.
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23
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Moskalev AА, Kudryavtseva AV, Graphodatsky AS, Beklemisheva VR, Serdyukova NA, Krutovsky KV, Sharov VV, Kulakovskiy IV, Lando AS, Kasianov AS, Kuzmin DA, Putintseva YA, Feranchuk SI, Shaposhnikov MV, Fraifeld VE, Toren D, Snezhkina AV, Sitnik VV. De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. BMC Evol Biol 2017; 17:258. [PMID: 29297306 PMCID: PMC5751776 DOI: 10.1186/s12862-017-1103-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Gray whale, Eschrichtius robustus (E. robustus), is a single member of the family Eschrichtiidae, which is considered to be the most primitive in the class Cetacea. Gray whale is often described as a “living fossil”. It is adapted to extreme marine conditions and has a high life expectancy (77 years). The assembly of a gray whale genome and transcriptome will allow to carry out further studies of whale evolution, longevity, and resistance to extreme environment. Results In this work, we report the first de novo assembly and primary analysis of the E. robustus genome and transcriptome based on kidney and liver samples. The presented draft genome assembly is complete by 55% in terms of a total genome length, but only by 24% in terms of the BUSCO complete gene groups, although 10,895 genes were identified. Transcriptome annotation and comparison with other whale species revealed robust expression of DNA repair and hypoxia-response genes, which is expected for whales. Conclusions This preliminary study of the gray whale genome and transcriptome provides new data to better understand the whale evolution and the mechanisms of their adaptation to the hypoxic conditions. Electronic supplementary material The online version of this article (doi: 10.1186/s12862-017-1103-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey А Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation. .,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russian Federation.
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, Novosibirsk, 630090, Russian Federation
| | | | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russian Federation
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, 37077, Germany.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of Ecosystem Science and Management, Texas A&M University, College Station, 77843-2138, TX, USA
| | - Vadim V Sharov
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Andrey S Lando
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Dmitry A Kuzmin
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation
| | - Yuliya A Putintseva
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation
| | - Sergey I Feranchuk
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Irkutsk National Research Technical University, Irkutsk, 664074, Russian Federation.,Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033, Russian Federation
| | - Mikhail V Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russian Federation
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Anastasia V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Vasily V Sitnik
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
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Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Plant J 2017; 91:278-291. [PMID: 28387959 DOI: 10.1111/tpj.13563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 05/22/2023]
Abstract
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
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Affiliation(s)
- Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
| | - Anna V Klepikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ivan V Kulakovskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Evgeny S Gerasimov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna V Fedotova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elizaveta G Besedina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA
| | - Maria D Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Klepikova AV, Kasianov AS, Chesnokov MS, Lazarevich NL, Penin AA, Logacheva M. Effect of method of deduplication on estimation of differential gene expression using RNA-seq. PeerJ 2017; 5:e3091. [PMID: 28321364 PMCID: PMC5357343 DOI: 10.7717/peerj.3091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.
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Affiliation(s)
- Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,N. I. Vavilov Institute for General Genetics, Moscow, Russia
| | - Mikhail S Chesnokov
- N.N. Blokhin Russian Cancer Research Center of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalia L Lazarevich
- N.N. Blokhin Russian Cancer Research Center of the Ministry of Health of the Russian Federation, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan
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Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J 2016; 88:1058-1070. [PMID: 27549386 DOI: 10.1111/tpj.13312] [Citation(s) in RCA: 388] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.
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Affiliation(s)
- Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Artem S Kasianov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res 2016; 44:D116-25. [PMID: 26586801 PMCID: PMC4702883 DOI: 10.1093/nar/gkv1249] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 02/06/2023] Open
Abstract
Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.
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Affiliation(s)
- Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia
| | - Ilya E Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia
| | - Ivan S Yevshin
- Design Technological Institute of Digital Techniques, Siberian Branch of the Russian Academy of Sciences, 630090, Academician Rzhanov 6, Novosibirsk, Russia Institute of Systems Biology Ltd, 630112, office 901, Krasina 54, Novosibirsk, Russia
| | - Anastasiia V Soboleva
- Moscow Institute of Physics and Technology, 141700, Institutskiy per. 9, Dolgoprudny, Moscow Region, Russia
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia
| | - Haitham Ashoor
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
| | - Wail Ba-Alawi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
| | - Yulia A Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia Center for Bioengineering, Russian Academy of Sciences, 117312, 60-letiya Oktyabrya 7/2, Moscow, Russia
| | - Fedor A Kolpakov
- Design Technological Institute of Digital Techniques, Siberian Branch of the Russian Academy of Sciences, 630090, Academician Rzhanov 6, Novosibirsk, Russia Institute of Systems Biology Ltd, 630112, office 901, Krasina 54, Novosibirsk, Russia
| | - Vsevolod J Makeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia Moscow Institute of Physics and Technology, 141700, Institutskiy per. 9, Dolgoprudny, Moscow Region, Russia
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Zakharevich NV, Averina OV, Klimina KM, Kudryavtseva AV, Kasianov AS, Makeev VJ, Danilenko VN. Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes. Microb Ecol 2015; 70:819-834. [PMID: 25894918 DOI: 10.1007/s00248-015-0603-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
In this study, we report the first completely annotated genome sequence of the Russia origin Bifidobacterium longum subsp. longum strain GT15. Comparative genomic analysis of this genome with other available completely annotated genome sequences of B. longum strains isolated from other countries has revealed a high degree of conservation and synteny across the entire genomes. However, it was discovered that the open reading frames to 35 genes were detected only from the B. longum GT15 genome and absent from other genomes B. longum strains (not of Russian origin). These so-called unique genes (UGs) represent a total length of 39,066 bp, with G + C content ranging from 37 to 65 %. Interestingly, certain genes were detected in other B. longum strains of Russian origin. In our analysis, we examined genes for global regulatory systems: proteins of toxin-antitoxin (TA) systems type II, serine/threonine protein kinases (STPKs) of eukaryotic type, and genes of the WhiB-like family proteins. In addition, we have made in silico analysis of all the most significant probiotic genes and considered genes involved in epigenetic regulation and genes responsible for producing various neuromediators. This genome sequence may elucidate the biology of this probiotic strain as a promising candidate for practical (pharmaceutical) applications.
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Affiliation(s)
| | - Olga V Averina
- Vavilov Institute of General Genetics, Gubkina str. 3, 119991, Moscow, Russia
| | - Ksenia M Klimina
- Vavilov Institute of General Genetics, Gubkina str. 3, 119991, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Vavilova str. 32, 119991, Moscow, Russia
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Gubkina str. 3, 119991, Moscow, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Gubkina str. 3, 119991, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Vavilova str. 32, 119991, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Gubkina str. 3, 119991, Moscow, Russia
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Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res 2012; 41:D195-202. [PMID: 23175603 PMCID: PMC3531053 DOI: 10.1093/nar/gks1089] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source.
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Affiliation(s)
- Ivan V Kulakovskiy
- Laboratory of Bioinformatics and Systems Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, GSP-1, Russia.
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Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. ACTA ACUST UNITED AC 2011; 27:2621-4. [PMID: 21852305 DOI: 10.1093/bioinformatics/btr453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. RESULTS We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3(')-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. CONTACT ivan.kulakovskiy@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- I V Kulakovskiy
- Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
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Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 2011; 12:30. [PMID: 21232141 PMCID: PMC3027159 DOI: 10.1186/1471-2164-12-30] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/13/2011] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, Fagopyrum esculentum and F. tataricum, belong to the order Caryophyllales--a large group of flowering plants with uncertain evolutionary relationships. F. esculentum (common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects. RESULTS Normalized cDNA corresponding to genes expressed in flowers and inflorescences of F. esculentum and F. tataricum was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for F. esculentum) and 229 (F. tataricum) thousands of reads with average length of 341-349 nucleotides. De novo assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences. CONCLUSIONS 454 transcriptome sequencing and de novo assembly was performed for two congeneric flowering plant species, F. esculentum and F. tataricum. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.
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Affiliation(s)
- Maria D Logacheva
- Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
| | - Artem S Kasianov
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy V Vinogradov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
| | - Tagir H Samigullin
- Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod J Makeev
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- N.I Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, Moscow, Russia
| | - Aleksey A Penin
- Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
- Department of Genetics, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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