Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice and Arabidopsis

Abstract

Photosynthesis uses sunlight and carbon dioxide to produce biomass that is vital to all life on earth. In seed plants, leaf is the main organ for photosynthesis and production of organic nutrients. The seeds are mobilized to fuel post-germination seedling growth until seedling photosynthesis can be efficiently established. However, the photosynthesis and metabolism in the early growth and development have not been studied systematically and are still largely unknown. In this study, we used two model plants, rice (Oryza sativa L.; monocotyledonous) and Arabidopsis (Arabidopsis thaliana; dicotyledonous) to determine the similarities and differences in photosynthesis in cotyledons and true leaves during the early developmental stages. The photosynthesis-related genes and proteins, and chloroplast functions were determined through RNA-seq, real-time PCR, western blotting and chlorophyll fluorescence analysis. We found that in rice, the photosynthesis established gradually from coleoptile (cpt), incomplete leaf (icl) to first complete leaf (fcl); whereas, in Arabidopsis, photosynthesis well-developed in cotyledon, and the photosynthesis-related genes and proteins expressed comparably in cotyledon (cot), first true leaf (ftl) and second true leaf (stl). Additionally, we attempted to establish an mRNA-lncRNA signature to explore the similarities and differences in photosynthesis establishment between the two species, and found that DEGs, including encoding mRNAs and novel lncRNAs, related to photosynthesis in three stages have considerable differences between rice and Arabidopsis. Further GO and KEGG analysis systematically revealed the similarities and differences of expression styles of photosystem subunits and assembly factors, and starch and sucrose metabolisms between cotyledons and true leaves in the two species. Our results help to elucidate the gene functions of mRNA-lncRNA signatures.

Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana

“…Previous works have already established the relationship between lncRNAs and processes related to photosynthesis in A. thaliana and rice [134], as well as in the response to different types of light [18,135]. Photosynthesis is arguably the most important biological pathway in plants.…”

RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.)

“…In addition, previous study showed that long-chain non-coding RNAs (lncRNAs) might participate in the carbohydrate metabolism. Shi et al (2020) reported that some lncRNAs is related to the expression regulation of key genes in starch and sucrose metabolisms, which participate in seedling development in rice and Arabidopsis. Although previous studies have shown that carbohydrates play an important role in post-mowing regeneration of wheat, the expression patterns of key genes and the changes in carbohydrate metabolism during this process remain unclear.…”

Characterization of the metabolic networks and gene-metabolite associations underlying cuticle production in maize via systems’ biology approaches

“…The establishment process of photosynthetic machinery during young seedling development from the time of germination is still not fully understood. Recently, photosynthesis establishment early in seedling growth has been compared between rice (monocotyledonous) and Arabidopsis (dicotyledonous), wherein photosynthesis in the monocot model establishes gradually from the coleoptile to the first leaf, but in the dicot model photosynthesis is welldeveloped in the cotyledons and maintains at a similar level throughout seedling development (Shi et al, 2020). Our gene expression study of maize seedlings, which are also monocotyledonous, are similar to observations in rice in that the up-regulation of photosynthesisrelated genes commences once the seedlings emerge above ground and continues in the leaves that sequentially develop from the shoot meristem.…”