Multi-omics analysis of early leaf development in Arabidopsis thaliana.
Ontology highlight
ABSTRACT:
SUBMITTER: Omidbakhshfard MA
PROVIDER: S-EPMC8085607 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The growth of plant organs is driven by cell division and subsequent cell expansion. The transition from proliferation into expansion is critical for the final organ size and, consequently plant yield. Exit from proliferation and onset of expansion is accompanied by major metabolic reprogramming, and in leaves with the establishment of photosynthesis. To learn more about the molecular mechanisms underlying the developmental and metabolic transitions important for plant growth, we used untargeted proteomics and metabolomics analyses to profile young leaves of a model plant Arabidopsis thaliana representing proliferation, transition, and expansion stages. The third true leaves of the in vitro grown Arabidopsis seedlings were harvested daily from day 8 to day 13 after stratification (8 to 13 DAS). Days 8 and 9 correspond to proliferation, days 12 and 13 to expansion and days 10 and 11 to the transition. The dataset presented represents a unique resource comprising approximately 4000 proteins and 300 annotated small-molecular compounds measured across six consecutive days of leaf growth. These can now be mined for novel developmental and metabolic regulators of plant growth and can act as a blueprint for future studies aimed at better defining the interface of development and metabolism in any other species.
2021-09-09 | PXD019545 | Pride
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Project description:BackgroundThe Leucine rich-repeat (LRR) receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others are involved in defence responses. However, functional data is currently only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function.ResultsUsing publicly available datasets, we annotated RLPs of unknown function as either likely defence-related or likely fulfilling a more basal function in plants. Then, using these categories, we can identify important characteristics that differ between the RLP subclasses. We found that the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic di versity of their individual members in accessible pan-genome data.ConclusionsOur work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions on which RLPs can be identified as potential immune receptors using genetics tools and thereby complement disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.
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