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Project description:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE122135 | GEO
Project description:In mammals, it is well known that DNA methylation has important roles during aging. However, age-related DNA methylation changes during phase transitions largely remain unclear in plants. Moso bamboo needs a very long time to transition from vegetative to floral phase. To comprehensively investigate the influence of DNA methylation on aging, we present here a distinctive single-base-resolution DNA methylation profile using both high-throughput bisulfite sequencing (BS-Seq) and single-molecule nanopore-based DNA sequencing, which covers the long period of vegetative growth and transition to flowering of moso bamboo’s development. We discovered that CHH methylation gradually accumulated from vegetative to reproductive growth in a time-dependent fashion. Importantly, DMR (differential DNA methylation) correlating with chronological aging occurred preferentially at both transcription start sites (TSS) and transcription termination sites (TTS). Genes with CG methylation changes showed enrichment of gene ontology (GO) categories in ‘vegetative to reproductive phase transition of meristem’. In addition, In combination with mRNA sequencing (RNA-Seq) revealed that DNA methylation in promoter, intron, and exon has different roles in regulating gene expression. Finally, circular RNA sequencing (circRNA-Seq) revealed that flanking introns of circRNAs show hypermethylation. Further analysis revealed that these flanking introns were enriched in LTR-retrotransponsons. Together, observations in this study provide insights about dynamic DNA methylation and circRNAs landscape with chronological ages, which paves the way to further study the impact of epigenetic factors on flowering in moso bamboo.
2021-04-30 | GSE139217 | GEO
Project description:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE121216 | GEO
Project description:Distinct DNA methylomes of moso bamboo in the phase transition from vegetative to reproductive growth
| PRJNA503816 | ENA
Project description:Distinct DNA methylomes of moso bamboo in the phase transition from vegetative to reproductive growth
| PRJNA578758 | ENA
Project description:Distinct transcriptomes and DNA methylomes of moso bamboo in the phase transition from vegetative to reproductive growth
| PRJNA503813 | ENA
Project description:Distinct transcriptome of moso bamboo in the phase transition from vegetative to reproductive growth
| PRJNA496390 | ENA
Project description:BackgroundMoso bamboo (Phyllostachys edulis) is a typical East Asian bamboo that does not flower for > 60 years and propagates without seed reproduction. Thus, Moso bamboo can be propagated vegetatively, possibly resulting in highly heterozygous genetic inheritance. Recently, a draft genome of Moso bamboo was reported, followed by whole genome single nucleotide polymorphisms (SNP) analysis, which showed that the genome of Moso bamboo in China has regional characteristics. Moso bamboo in Japan is thought to have been introduced from China over the sea in 1736. However, it is unclear where and how Moso bamboo was introduced in Japan from China. Here, based on detailed analysis of heterozygosity in genome diversity, we estimate the spread of genome diversity and its pedigree of Moso bamboo.ResultsWe sequenced the whole genome of Moso bamboo in Japan and compared them with data reported previously from 15 regions of China. Only 4.1 million loci (0.37% of the analyzed genomic region) were identified as polymorphic loci. We next narrowed down the number of polymorphic loci using several filters and extracted more reliable SNPs. Among the 414,952 high-quality SNPs, 319,431 (77%) loci were identified as heterozygous common to all tested samples. The result suggested that all tested samples were clones via vegetative reproduction. Somatic mutations may accumulate in a heterozygous manner within a single clone. We examined common heterozygous loci between samples from Japan and elsewhere, from which we inferred that an individual closely related to the sample from Fujian, China, was introduced to Japan across the sea without seed reproduction. In addition, we collected 16 samples from four nearby bamboo forests in Japan and performed SNP and insertion/deletion analyses using a genotyping by sequencing (GBS) method. The results suggested that a small number of somatic mutations would spread within and between bamboo groves.ConclusionsHigh heterozygosity in the genome-wide diversity of Moso bamboo implies the vegetative propagation of Moso bamboo from China to Japan, the pedigree of Moso bamboo in Japan, and becomes a useful marker to approach the spread of genome diversity in clonal plants.
| S-EPMC10290394 | biostudies-literature
Project description:BackgroundFor plants to flower at the appropriate time, they must be able to perceive and respond to various internal and external cues. Wheat is generally a long-day plant that will go through phase transition from vegetative to floral growth as days are lengthening in spring and early summer. In addition to this response to day-length, wheat cultivars may be classified as either winter or spring varieties depending on whether they require to be exposed to an extended period of cold in order to become competent to flower. Using a growth regime to mimic the conditions that occur during a typical winter in Britain, and a microarray approach to determine changes in gene expression over time, we have surveyed the genes of the major pathways involved in floral transition. We have paid particular attention to wheat orthologues and functional equivalents of genes involved in the phase transition in Arabidopsis. We also surveyed all the MADS-box genes that could be identified as such on the Affymetrix genechip wheat genome array.ResultsWe observed novel responses of several genes thought to be of major importance in vernalisation-induced phase transition, and identified several MADS-box genes that might play an important role in the onset of flowering. In addition, we saw responses in genes of the Gibberellin pathway that would indicate that this pathway also has some role to play in phase transition.ConclusionPhase transition in wheat is more complex than previously reported, and there is evidence that day-length has an influence on genes that were once thought to respond exclusively to an extended period of cold.
| S-EPMC2685395 | biostudies-literature