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Transcriptome atlas of Phalaenopsis equestris [article]

Anna V Klepikova, Artem S Kasianov, Margarita A Ezhova, Aleksey A Penin, Maria D Logacheva
2020 bioRxiv   pre-print
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 which covers 19 organs of the plant including leaves, roots, floral organs and shoot apical meristem. We demonstrated the high quality of the data and showed
more » ... he similarity of P. equestris transcriptome map with gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) visualizing gene expression profiles. As an example of the application we analyzed the expression of Phalaenopsis "orphan" genes - the ones that do not have recognizable similarity with genes of other plants. We found that about a half of them are not expressed; the ones that are expressed have a predominant expression pattern in reproductive structures.
doi:10.1101/2020.11.03.366260 fatcat:ygakxbt5yzbx7dlteaeejchr5a

Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19 [article]

Anna A. Valyaeva, Anastasia A. Zharikova, Artem S. Kasianov, Yegor S. Vassetzky, Eugene V. Sheval
2020 biorxiv/medrxiv   pre-print
., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T.S., Herrler, G., Wu, N.-H., Nitsche, A., et al. (2020a).  ...  Cellular entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and on S protein priming by host cell proteases.  ... 
doi:10.1101/2020.05.23.107334 fatcat:2lltbgu4hnhepmdkpdvrtebnhm

Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum

Aleksey A. Penin, Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, Maria D. Logacheva
2019 Genes  
Annotation SL2.50 of the S. lycopersicum genome contains 33,810 coding genes.  ...  Genome assembly for S. lycopersicum was taken from the Ensembl database: assembly and corresponding annotation version SL2.50.  ... 
doi:10.3390/genes10010050 pmid:30650673 pmcid:PMC6356586 fatcat:scy6enziqjhtrex566k44fdcc4

Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

Denis O. Omelchenko, Maxim S. Makarenko, Artem S. Kasianov, Mikhail I. Schelkunov, Maria D. Logacheva, Aleksey A. Penin
2020 Plants  
calling results of the mapped data generated by bcftools 1.9 (with settings "mpilepup -I -B -d 8000" and then "call -m -V indels -Ov") [40, 41] and the REDO script [42] with settings "-d 30 -c 10 -s  ... 
doi:10.3390/plants9040469 pmid:32276324 fatcat:km7de77fbjbxjm2avgxikghaiq

Rapid accumulation of mutations in growing mycelia of a hypervariable fungus Schizophyllum commune [article]

Aleksandra V Bezmenova, Elena A Zvyagina, Anna V Fedotova, Artem S Kasianov, Tatiana V Neretina, Aleksey A Penin, Georgii A Bazykin, Alexey S Kondrashov
2019 bioRxiv   pre-print
We show that S. commune accumulates mutations at a uniform rate of 1.4·10-7 substitutions per nucleotide per meter of growth, which is 3 orders of magnitude higher than the corresponding rates in the oak  ...  S. commune .  ...  a 1 m S. commune (5.4 substitutions) .  ... 
doi:10.1101/781310 fatcat:nlap3znpwrhxjmkgkfxqx3dqze

High-resolution transcriptome atlas and improved genome assembly of common buckwheat, Fagopyrum esculentum [article]

Aleksey A Penin, Artem S Kasianov, Anna V Klepikova, Ilya V Kirov, Evgeny S Gerasimov, Aleksey N Fesenko, Maria D Logacheva
2020 bioRxiv   pre-print
the genes with broadest and narrowest expression patterns Table S9 Buckwheat MYB genes selected based on similarity to MIXTA and MYB16/MYB106 of F. esculentum compared with those of A. thaliana and S.  ... 
doi:10.1101/2020.11.14.382903 fatcat:xxrcptzhhzaitd4wuxspjdqewm

Effect of method of deduplication on estimation of differential gene expression using RNA-seq

Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Natalia L. Lazarevich, Aleksey A. Penin, Maria Logacheva
2017 PeerJ  
ACKNOWLEDGEMENTS The authors are grateful to Alexey S. Kondrashov for proofreading and editing the manuscript.  ...  A total of 45 cycles of amplification (30 s at 95 • C, 30 s at annealing temperature (Table S4) , 30 s at 72 • C) were performed and reaction specificity was checked by melt curve analysis.  ...  . • Artem S. Kasianov analyzed the data, prepared figures and/or tables. • Mikhail S. Chesnokov performed the experiments. • Natalia L.  ... 
doi:10.7717/peerj.3091 pmid:28321364 pmcid:PMC5357343 fatcat:xnw7yvxqfvax3hqxhxyhjaadxi

Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat

Maria D. Logacheva, Mikhail I. Schelkunov, Aleksey N. Fesenko, Artem S. Kasianov, Aleksey A. Penin
2020 Plants  
We hypothesize that this mutation(s) increases the photosynthesis efficiency and their fixation in buckwheat cultivars is the result of artificial selection.  ... 
doi:10.3390/plants9050618 pmid:32408719 pmcid:PMC7285332 fatcat:nzf3h23vh5h6zgygmrsbaq6d7m

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana

Anna V. Klepikova, Ivan V. Kulakovskiy, Artem S. Kasianov, Maria D. Logacheva, Aleksey A. Penin
2019 BMC Plant Biology  
[5] and Kasianov et al. [10] .  ... 
doi:10.1186/s12870-019-1636-y fatcat:cycbw4okvnhyxfd4fr4os2r7yu

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum

Aleksey A. Penin, Artem S. Kasianov, Anna V. Klepikova, Ilya V. Kirov, Evgeny S. Gerasimov, Aleksey N. Fesenko, Maria D. Logacheva
2021 Frontiers in Plant Science  
FIGURE 1 | 1 FIGURE 1 | (À) Annotation of F. esculentum compared with those of A. thaliana and S. lycopersicum in terms of the gene, exon, and intron length distribution.  ...  It has carpelloid organs instead of tepals, presumably due to the overexpression of C-class gene(s); in case if B-class genes had been involved these would have been stamens.  ... 
doi:10.3389/fpls.2021.612382 pmid:33815435 pmcid:PMC8010679 fatcat:6hrbiphxxbcx5nucd5teuajq5q

Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles

Andrey D. Novikov, Konstantin V. Lavrov, Artem S. Kasianov, Tatyana V. Gerasimova, Alexander S. Yanenko
2018 Genome Announcements  
Accession number(s). This whole-genome shotgun sequence has been deposited at GenBank/DDBJ/EMBL under the accession no. MLYX00000000.  ...  S ynthetic nitriles are widely employed in organic synthesis as precursors of various amides and acids, which are obtained via hydration of the triple C-N bond in the nitriles (1, 2) .  ... 
doi:10.1128/genomea.01526-17 pmid:29439044 pmcid:PMC5805882 fatcat:w2sia46jfzdvjggj5ryfn4vn7a

Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota

Ksenia M. Klimina, Viktoriya N. Voroshilova, Elena U. Poluektova, Vladimir A. Veselovsky, Roman A. Yunes, Aleksey S. Kovtun, Anna V. Kudryavtseva, Artem S. Kasianov, Valery N. Danilenko
2020 Toxins  
(Artem S. Kasianov); validation, V.N.V., V.A.V. and A.S.K. (Aleksey S. Kovtun); formal analysis, A.S.K. (Artem S.  ...  (Artem S. Kasianov) and V.N.D.; project administration, K.M.K.; funding acquisition, K.M.K. All authors have read and agreed to the published version of the manuscript.  ... 
doi:10.3390/toxins12060388 pmid:32545455 fatcat:od37jg7gsvda7djxk3q5rsk6ey

An Update to the TraVA Database: Time Series of Capsella bursa-pastoris Shoot Apical Meristems during Transition to Flowering

Anna V. Klepikova, Artem S. Kasianov
2020 Data  
Transition to flowering is a crucial part of plant life directly affecting the fitness of a plant. Time series of transcriptomes is a useful tool for the investigation of process dynamics and can be used for the identification of novel genes and gene networks involved in the process. We present a detailed time series of polyploid Capsella bursa-pastoris shoot apical meristems created with RNA-seq. The time series covers transition to flowering and can be used for thorough analysis of the
more » ... . To make the data easy to access, we uploaded them in our database Transcriptome Variation Analysis (TraVA), which provides a convenient depiction of the gene expression profiles, the differential expression analysis between the homeologs and quick data extraction.
doi:10.3390/data5030058 fatcat:qhgkyuvpnrfpjn3ynbabn4q4q4

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

Maria D Logacheva, Artem S Kasianov, Dmitriy V Vinogradov, Tagir H Samigullin, Mikhail S Gelfand, Vsevolod J Makeev, Aleksey A Penin
2011 BMC Genomics  
Finally, the number of false positives was calculated as Σ k(j,s) p(0,j,s) where k(j,s) is the total number of genes with j reads in species s.  ...  First, the probability p(i,j,s) to observe i reads for the gene in one species (s) given j reads for its ortholog in the other species was calculated.  ... 
doi:10.1186/1471-2164-12-30 pmid:21232141 pmcid:PMC3027159 fatcat:oppuheuf65e5jmjsmcps54r6c4

Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production

Andrey D. Novikov, Konstantin V. Lavrov, Artem S. Kasianov, Maxim A. Topchiy, Tatyana V. Gerasimova, Alexander S. Yanenko, J. Cameron Thrash
2021 Microbiology Resource Announcements  
We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.
doi:10.1128/mra.01314-20 pmid:33707335 fatcat:32pqpsixk5culo3z6nqyh4e4uu
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