Saccharum officinarum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12961 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| JAIWYO01.dat.gz | Other | |||
| JAIWYO01.fasta.gz | Fasta.gz | |||
| JAIWYO01.master.dat | Other | |||
| JAQSUU01.dat.gz | Other |
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Project description:BACKGROUND:Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. RESULTS:In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. CONCLUSIONS:SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.
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Project description:Divergence in the effects of sugar feedback regulation on the major gene regulatory network and metabolism of photosynthesis in leaves between the two founding Saccharum species
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Project description:Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.
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Project description:The widely reported anti-androgenic effects of refined sugar led to the exploration of safer alternatives. Saccharum officinarum molasses (SOM), a byproduct of sugar processing is gaining popularity as a substitute. This study investigated the effects of SOM and compared them to those of refined sugar on male reproductive functions. Blackstrap® Saccharum officinarum molasses were subjected to phytochemical screening and proximate analysis and fractionated to obtain methanol (SOMMF) and aqueous (SOMAqF) fractions. Twelve groups (n?=?5) of adult male Wistar rats received distilled water (Control); 0.8, 2.5, 7.9?g/kg SOM; 0.0064?g/kg sugar (Dangote®); 0.0064?g/kg sugar+7.9?g/kg SOM; 1.0, 3.2, 10.0?g/kg SOMMF and 0.6, 2.0, 6.4?g/kg SOMAqF, respectively. Administrations were done daily by oral gavage for eight weeks. Sperm profile and testicular and epididymal histology were assessed using microscopy. Serum testosterone was quantified using ELISA. Testicular malondialdehyde (MDA) was assayed by spectrophotometry. Data were analyzed using ANOVA at p?<?0.05 significance. Sperm count and viability reduced with 7.9?g/kg SOM, Sugar, 3.2 and 10.0?g/kg SOMMF, 2.0 and 6.4?g/kg SOMAqF. Abnormal sperms increased with 7.9?g/kg SOM, Sugar, 2.0 and 6.4?g/kg SOMAqF. Testosterone level reduced with 6.4?g/kg SOMAqF. Testicular MDA increased with SOM, 3.2 and 10.0?g/kg SOMMF and 6.4?g/kg SOMAqF. Seminiferous tubules and epididymal ducts of 7.9?g/kg SOM, Sugar and SOMAqF-treated rats showed anomalies. Saccharum officinarum molasses altered testicular and epididymal integrity via lipid peroxidation, thus reducing sperm quality and androgen levels in male Wistar rats.
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Project description:The finite nature, regional availability, and environmental
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Project description:Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80-90% of the genome from S. officinarum and 10-20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.
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