Promising markers of CIMP+ colon tumors identified on the basis of TCGA data analysis

CIMP+ (CpG­Island Methylator Phenotype) tumors are characterized by dense methylation of promoter CpG islands of many genes at once and represent a separate group of malignant neoplasms of the colon. Despite the fact that the diagnostics of CIMP+ tumors has a significant prognostic value, an effective set of markers has not been developed yet. For the identification of CpG sites, the methylation level of which could be used to detect CIMP+ tumors, an analysis of expression and methylation profiles of 297 primary colon tumors and 38 histologically normal tissues paired to them, which are presented in the TCGA (The Cancer Genome Atlas) project database, was performed by us using the CrossHub tool created previously. We developed the scoring, which takes into account the methylation level of CpG sites, their location, and the expression level of the corresponding genes. It was revealed that the methylation status of CpG sites of the AMOTL1, ZNF43, ZNF134, and CHFR genes is a promising marker of CIMP+ tumors. Moreover, specific regions of promoters of these genes, the methylation level of which was associated with the examined phenotype, were identified. To verify the obtained data in independent sampling, first, the quantitative PCR was used to assess the relative mRNA level of the AMOTL1, ZNF43, ZNF134, and CHFR genes in 30 paired (tumor/histologically normal tissue) colon samples. For all the genes, a frequent (50–60 % of cases) and significant (2–30­fold) expression decrease was revealed. Then, the bisulfite conversion of DNA followed by cloning and sequencing was applied to examine the methylation status of CpG sites that were selected as the result of bioinformatics analysis. We observed a high methylation level (β­value = 0.3–0.9) of the CpG sites in the samples with simultaneous downregulation of all 4 genes and a low methylation level (β­value = 0.0–0.2) in the samples with the unchanged expression level of 4 genes and in histologically normal tissues. Thus, the methylation status of the CpG sites of promoter regions of the AMOTL1, ZNF43, ZNF134, and CHFR genes is a promising potential marker of CIMP+ colon tumors

The cinnamyl alcohol dehydrogenase gene family is involved in the response to Fusarium oxysporum in resistant and susceptible flax genotypes

Flax (Linum usitatissimum L.) is used for the production of textile, oils, pharmaceuticals, and composite materials. Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. lini, is a very harmful disease that reduces flax production. Flax cultivars that are resistant to Fusarium wilt have been developed, and the genes that are involved in the host response to F. oxysporum have been identified. However, the mechanisms underlying resistance to this pathogen remain unclear. In the present study, we used transcriptome sequencing data obtained from susceptible and resistant flax genotypes grown under control conditions or F. oxysporum infection. Approximately 250 million reads, generated with an Illumina NextSeq instrument, were analyzed. After filtering to exclude the F. oxysporum transcriptome, the remaining reads were mapped to the L. usitatissimum genome and quantified. Then, the expression levels of cinnamyl alcohol dehydrogenase (CAD) family genes, which are known to be involved in the response to F. oxysporum, were evaluated in resistant and susceptible flax genotypes. Expression alterations in response to the pathogen were detected for all 13 examined CAD genes. The most significant differences in expression between control and infected plants were observed for CAD1B, CAD4A, CAD5A, and CAD5B, with strong upregulation of CAD1B, CAD5A, and CAD5B and strong downregulation of CAD4A. When plants were grown under the same conditions, the expression levels were similar in all studied flax genotypes for most CAD genes, and statistically significant differences in expression between resistant and susceptible genotypes were only observed for CAD1A. Our study indicates the strong involvement of CAD genes in flax response to F. oxysporum but brings no evidence of their role as resistance gene candidates. These findings contribute to the understanding of the mechanisms underlying the response of flax to F. oxysporum infection and the role of CAD genes in stress resistance

Genome of Linum usitatissimum convar. crepitans expands the view on the section Linum

Sequencing whole plant genomes provides a solid foundation for applied and basic studies. Genome sequences of agricultural plants attract special attention, as they reveal information on the regulation of beneficial plant traits. Flax is a valuable crop cultivated for oil and fiber. Genome sequences of its representatives are rich sources of genetic information for the improvement of cultivated forms of the plant. In our work, we sequenced the first genome of flax with the dehiscence of capsules—Linum usitatissimum convar. сrepitans (Boenn.) Dumort—on the Oxford Nanopore Technologies (ONT) and Illumina platforms. We obtained 23 Gb of raw ONT data and 89 M of 150 + 150 paired-end Illumina reads and tested different tools for genome assembly and polishing. The genome assembly produced according to the Canu—Racon ×2—medaka—POLCA scheme had optimal contiguity and completeness: assembly length—412.6 Mb, N50—5.2 Mb, L50—28, and complete BUSCO—94.6% (64.0% duplicated, eudicots_odb10). The obtained high-quality genome assembly of L. usitatissimum convar. crepitans provides opportunities for further studies of evolution, domestication, and genome regulation in the section Linum

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

TRY plant trait database - enhanced coverage and open access

This article has 730 authors, of which I have only listed the lead author and myself as a representative of University of HelsinkiPlant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.Peer reviewe

TRY plant trait database - enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Hydrometeorological Database (HMDB) for Practical Research in Ecology

The regional HydroMeteorological DataBase (HMDB) was designed for easy access to climate data via the Internet. It contains data on various climatic parameters (temperature, precipitation, pressure, humidity, and wind strength and direction) from 190 meteorological stations in Russia and bordering countries for a period of instrumental observations of over 100 years. Open sources were used to ingest data into HMDB. An analytical block was also developed to perform the most common statistical analysis techniques

Ecological and habitat ranges of orchids in the northernmost regions of their distribution areas: A case study from Ural Mountains, Russia

The Orchidaceae, which is one of the most interesting families of angiosperms, contains a large number of rare species. Despite their acknowledged importance, little attention has been paid to the study of orchids distributed in northern territories. In this study, we determined the syntaxonomical diversity and ecological parameters of orchid habitats in two of Europe's largest protected areas, the Pechoro-Ilychsky Reserve and the Yugyd Va National Park (northeastern European Russia), and then compared our findings to those in other parts of orchid distribution ranges. For this purpose, we studied 345 descriptions of plant communities (releves) containing species from Orchidaceae and defined habitat parameters using Ellenberg indicator values with the community weight mean approach, nonmetric multidimensional scaling (NMS), and relative niche width. We found that orchids were distributed in eight habitat types and 97 plant associations. The largest number of orchid species is found in forest communities. Half of the orchid species under study occur in the mires and rock habitats with open vegetation. Several orchids consistently occur in areas disturbed by human activity. In addition, our study indicates that the main drivers of orchid distribution across the vegetation types are light and soil nitrogen. Our analysis of the ecological parameters of orchid habitats indicates that some orchid species can be classified as habitat specialists that are confined to a relatively narrow ecological niche in the Urals (e.g., Goodyera repens, Cypripedium guttatum and Dactylorhiza maculata). Several other species (e.g. Neottia cordata and Dactylorhiza fuchsia) grow under diverse ecological parameters