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Transcriptome sequencing and expression analysis of green sulcus and yellow culm in Phyllostachys violascens cv. Viridisulcata

ABSTRACT: In this study, we performed transcriptomics across P. violascens to identify the main pigments contributing to colorful culm and try to reveal a plausible transcriptional regulatory mechanism. The green sulci and yellow culms were collected from the middle of three bamboo’s longest internodes and the chosen bamboos were approximately in the same size which were both 3 meters high, in April 24, 2019. A total of 1,163,327,390 clean reads representing a total of 174.49 Gb nucleotides were generated, with an average GC content of 48.03%. A total 421 differentially expressed genes were identified in the pool.

ORGANISM(S): Phyllostachys violascens

PROVIDER: GSE157799 | GEO | 2022/02/18

REPOSITORIES: GEO

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Project description:Sugarcane is an economically important crop contributing to the world’s sugar and ethanol production with 80% and 40%, respectively. In recent years, the growing demands for sugar and ethanol production has prompted the necessity to increase sugarcane productivity through conventional breeding programs. However, sugarcane breeders have encountered several difficulties to raise productivity, mainly due to its complex genetics. Sugarcane has a polyploidy genome, with many varieties being aneuploidy. Today, the majority of the planted sugarcane cultivars are complex hybrids derived mainly from crosses between Saccharum officinarum and S. spontaneum. Therefore, proteomics can provide some insight into deciphering gene regulation and changes in carbon metabolism and sucrose accumulation in the culms at different stages of plant development. The aim of this work was to compare the quantitative changes of proteins in sugarcane culms, during plant growth and sucrose accumulation. Total proteins were isolated from both, juvenile and maturing internodes at three stages of plant development. Label free shotgun proteomics was used for protein profiling and quantification. The internodes 5 (I5) and 9 (I9) of 4, 7 and 10 month-old-plants (4M, 7M and 10M, respectively) were harvested and used for proteomic analyses. To mimic field conditions of sucrose accumulation during sugarcane maturation, we stopped watering 10M plants for 10 days. An average of 1130 proteins, unique and differentially expressed across all ages were identified and quantified. Proteins were categorized within 27 functional groups, related to biological process. The patterns of expression for some categories, such as cellular amino acids, metabolic processes, secondary metabolic processes and translation were down-regulated in the immature internode (I5-10M), while up-regulated in the mature I9-10M. We observed an increase in the abundance of several enzymes of the glycolytic pathway and isoforms of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC), in the juvenile stages of development of I9. These changes in enzymes contents indicates that at the early stages of internode development, hypoxia is increasing the glycolytic and ethanolic fermentation pathways, in order to supply ATP for plant growth and NAD+ for mitochondrial respiration, which might be impaired by the low oxygen availability inside the culm.

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Transcriptome sequencing and expression analysis of green sulcus and yellow culm in Phyllostachys violascens cv. Viridisulcata

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