The y-axis shows the number of experiments (in logarithmic scale) per species ( x-axis). (B) Transcriptomic h index for Viridiplantae. The y-axis indicates the number of samples deposited in the National Center for Biotechnology Information Sequence Read Archive (in logarithmic scale) per year from 2008 to 2021 ( x-axis). (A) Number of available RNA-seq data from different sequencing platforms. Conversely, certain insights are only observed in a specific clade of plants (vascular plants, exemplified by the gray circles), suggesting a punctuated appearance of the underlying transcriptional and genomic program or network rewiring of ancestral genes.Īvailability and types of transcriptomic data in plants For example, features that are observable in algae, bryophytes, and ferns but not in the flowering plants (represented by the golden circles) suggest that the genes and transcriptional programs that underlie these insights have been lost in the ancestors of flowering plants. The (C) ‘evolutionary insights’ are drawn from the patterns observed in the phylogeny of the feature. We term these (B) ‘robust insights’ because they are independently observed in more than one species. Certain insights will be observed in multiple species (e.g., ‘gene A in Arabidopsis is expressed in roots, and so is its homolog from rice’). The analysis of transcriptomic data can generate insights into (A) organ-specific gene expression (single species), (B) conservation (multiple species), and (C) gene evolution (species from different clades).
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