SummaryThe blue stain fungus Grosmannia clavigera (G. clavigera) is a pathogen of pines that can tolerate monoterpenes in oleoresin. Grosmannia clavigera has developed several mechanisms to cope with the host's monoterpene defence: a monoterpene efflux system mediated by an ABC transporter and enzymes that utilize or modify monoterpenes. In this study, we integrated two expression data sets based on a match between their multidimensional distributions. The data sets are raw RNA-seq and already processed transcriptome expression data with partially matching biological conditions. As a result, several new regulatory mechanisms, including the upregulation of the stress response and the developmental process at early-time-point terpene treatment, were involved in the adaptation of G. clavigera to monoterpenes and were supported by both data sets. In addition, several genes related to terpenoid modification were upregulated within 36 h (in rich media) and 7 days (in poor media) of terpene treatment. These results led us to the assumption that G. clavigera used terpenes as an energy source within 7 days when no other energy source was available, while within 36 h of terpene treatment on rich media these genes took part in terpene detoxification. As the G. clavigera genome is not well annotated, we performed detection of new putative transcripts as genome fragments enriched by read mapping. Several newly detected transcripts annotated as putative retrotransposons were upregulated mostly under early-time-point terpene treatment, while others annotated as putative ribonuclease and protease were downregulated mostly during early-time-point terpene treatment. Based on these results, it can be hypothesized that these new transcripts could play a role in previously unidentified G. clavigera terpene response regulatory mechanisms. Overall, this study identified gene expression regulations supported by two data sets as well as new putative transcripts related to new processes that might be important for G. clavigera tolerance to terpenes.
The climate changes across geological time are mirrored in paleontological fossils of stomata morphology. Professor Krassilov significantly contributed to a study of stomata development in modern plants. As a continuation of his work we ap proached the stomata regulation problem in modern plants by mining of the pub lically available transcriptome data on regulation of the stomata movement and formation by three of key regulators: SOC1, SPEECHLESS, and YODA. A goal of the study was to integrate heterogeneous data collections on stomata re gu lation and disclose the underlying basic regulation pathways that belong to sto mata as the specific cell type independently on perturbations of its regulatory path ways. By a fresh algorithmic approach, we managed to extract the underlying sto mata regulation genes from divergently designed stomata projects. In par ti cu lar, we defined groups of genes associated with the stomata patterning, for ma tion, and movement. Additionally, groups of genes were associated with specific pairs of these processes. Р Е З Ю М ЕМуха Д., Острецов Б., Муха Дм., Бродский Л. Механизмы образова-ния и функционирования устьичного аппарата используют одни и те же регуляторные гены. Изменения климата в геологическом време ни находят отражение в морфологии устьиц палеонтологических окаме нелостей. Профессор В.А. Красилов внес значительный вклад в изучение формирования устьиц современных растений. В развитие его идей мы по дошли к проблеме регуляции работы устьичного аппарата современных растений, проанализировав массив имеющихся данных по транскрибиро ванию функционирования и образования устьичного аппарата тремя клю чевыми регуляторами: SOC1, SPEECHLESS и YODA. Цель исследования -интегрировать разнородные данные по регулированию работы устьиц и раскрыть основные пути контроля устьиц, не зависящие от специфических особенностей регуляторных механизмов. С использованием нового алго ритмического подхода нам удалось определить основные регуляторные гены, ассоциированные с устьичным аппаратом, используя разнородные экспериментальные данные. В частности, мы определили группы генов, ассоциированных с расположением, формированием и функционирова нием устьиц. Кроме того, нами определены группы генов, вовлеченные в несколько регуляторных процессов одновременно.
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