Integrative transcriptomics and proteomics analysis constructs a new molecular model for ovule abortion in the female-sterile line of Pinus tabuliformis Carr.

Zhang, Min; Li, Wenhai; Feng, Jun; Gong, Zaixin; Yao, Yang; Zheng, Caixia

doi:10.1016/j.plantsci.2020.110462

Cited by 9 publications

(7 citation statements)

References 95 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The extraction of biologically meaningful patterns using data integration is now emerging as one of the most evolving fields in modern data science but there are very few such studies for plants ( Ding et al, 2020 ; Zhang et al, 2020 ). This work began with an aim to identify and investigate the plant prionome in order to explore a general role in memory based on the previous but limited reports of PrLPs having a role in flowering and plant memory.…”

Section: Discussionmentioning

confidence: 99%

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

et al. 2021

View full text Add to dashboard Cite

Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its “prionome.” In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.

show abstract

Section: Discussionmentioning

confidence: 99%

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

et al. 2021

View full text Add to dashboard Cite

show abstract

“…RFC 4, gag-pol , integrase, and KK1_037587 were involved in DNA replication and integration ( Table 1 ; Supplementary Tables S2, S3 ). RFC4 is a subunit of RFC , which might have a significant in A. thaliana embryo development, with embryonic lethality observed in AtRFC mutants ( Zhang et al, 2020a ). The rglB gene is involved in the carbohydrate metabolic process and catalytic activity.…”

Section: Discussionmentioning

confidence: 99%

A Bivariate Mapping Model Identifies Major Covariation QTLs for Biomass Allocation Between Leaf and Stem Growth of Catalpa bungei

Zhang

Zhu

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

Biomass allocation plays a critical role in plant morphological formation and phenotypic plasticity, which greatly impact plant adaptability and competitiveness. While empirical studies on plant biomass allocation have focused on molecular biology and ecology approaches, detailed insight into the genetic basis of biomass allocation between leaf and stem growth is still lacking. Herein, we constructed a bivariate mapping model to identify covariation QTLs governing carbon (C) allocation between the leaves and stem as well as the covariation of traits within and between organs in a full-sib mapping population of C. bungei. A total of 123 covQTLs were detected for 23 trait pairs, including six leaf traits (leaf length, width, area, perimeter, length/width ratio and petiole length) and five stem traits (height, diameter at breast height, wood density, stemwood volume and stemwood biomass). The candidate genes were further identified in tissue-specific gene expression data, which provided insights into the genetic architecture underlying C allocation for traits or organs. The key QTLs related to growth and biomass allocation, which included UVH1, CLPT2, GAD/SPL, COG1 and MTERF4, were characterised and verified via gene function annotation and expression profiling. The integration of a bivariate Quantitative trait locus mapping model and gene expression profiling will enable the elucidation of genetic architecture underlying biomass allocation and covariation growth, in turn providing a theoretical basis for forest molecular marker-assisted breeding with specific C allocation strategies for adaptation to heterogeneous environments.

show abstract

“…Using metabolomic studies, researchers can significantly increase the value of existing data, and multigroup analysis has become a powerful tool in recent years [24,31,32]. Combined analysis of transcriptome and proteome provided the basis for the molecular regulation of ovule development in gymnosperms [33], whereas metabolomics combined with potential target prediction, degradome validation, and transcriptome sequencing can expand our knowledge of metabolite profiling and potential functional roles in gymnosperm pollination drops [34]. Transcriptome and metabonomic analysis revealed the metabolic variation in sex differences in Ginkgo biloba L. [35].…”

Section: Discussionmentioning

confidence: 99%

Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Fan

Zhang

et al. 2020

Forests

View full text Add to dashboard Cite

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

show abstract

Integrative transcriptomics and proteomics analysis constructs a new molecular model for ovule abortion in the female-sterile line of Pinus tabuliformis Carr.

Cited by 9 publications

References 95 publications

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

A Bivariate Mapping Model Identifies Major Covariation QTLs for Biomass Allocation Between Leaf and Stem Growth of Catalpa bungei

Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Contact Info

Product

Resources

About