Dataset Information

CSCS: a chromatin state interface for Chinese Spring bread wheat.

ABSTRACT: A chromosome-level genome assembly of the bread wheat variety Chinese Spring (CS) has recently been published. Genome-wide identification of regulatory elements (REs) responsible for regulating gene activity is key to further mechanistic studies. Because epigenetic activity can reflect RE activity, defining chromatin states based on epigenomic features is an effective way to detect REs. Here, we present the web-based platform Chinese Spring chromatin state (CSCS), which provides CS chromatin signature information. CSCS includes 15 recently published epigenomic data sets including open chromatin and major chromatin marks, which are further partitioned into 15 distinct chromatin states. CSCS curates detailed information about these chromatin states, with trained self-organization mapping (SOM) for segments in all chromatin states and JBrowse visualization for genomic regions or genes. Motif analysis for genomic regions or genes, GO analysis for genes and SOM analysis for new epigenomic data sets are also integrated into CSCS. In summary, the CSCS database contains the combinatorial patterns of chromatin signatures in wheat and facilitates the detection of functional elements and further clarification of regulatory activities. We illustrate how CSCS enables biological insights using one example, demonstrating that CSCS is a highly useful resource for intensive data mining. CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.

Supplementary information

The online version contains supplementary material available at 10.1007/s42994-021-00048-z.

SUBMITTER: Ran X

PROVIDER: S-EPMC9590471 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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CSCS: a chromatin state interface for Chinese Spring bread wheat.

Ran Xiaojuan X Tang Tengfei T Wang Meiyue M Ye Luhuan L Zhuang Yili Y Zhao Fei F Zhang Yijing Y

aBIOTECH 20210531 4

A chromosome-level genome assembly of the bread wheat variety Chinese Spring (CS) has recently been published. Genome-wide identification of regulatory elements (REs) responsible for regulating gene activity is key to further mechanistic studies. Because epigenetic activity can reflect RE activity, defining chromatin states based on epigenomic features is an effective way to detect REs. Here, we present the web-based platform Chinese Spring chromatin state (CSCS), which provides CS chromatin sig ...[more]

PMID: 36311809

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Project description:BackgroundConventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.ResultsMetabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not.ConclusionsThe consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

Dataset Information

CSCS: a chromatin state interface for Chinese Spring bread wheat.

Supplementary information

Publications

CSCS: a chromatin state interface for Chinese Spring bread wheat.

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