Auxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso ...bamboo which is famous for its fast growth resulting from the rapid cell elongation and division.
Here we showed that exogenous auxin has strong effects on crown and primary roots. Genes involved in auxin action, including 13 YUCCA (YUC) genes involved in auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) and 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) members involved in auxin transport, 10 auxin receptors (AFB) involved in auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) genes, and 41 auxin response factors (ARF) involved in auxin signaling were identified through genome-wide analysis. Phylogenetic analysis of these genes from Arabidopsis, Oryza sativa and bamboo revealed that auxin biosynthesis, transport, and signaling pathways are conserved in these species. A comprehensive study of auxin-responsive genes using RNA sequencing technology was performed, and the results also supported that moso bamboo shared a conserved regulatory mechanism for the expression of auxin pathway genes; meanwhile it harbors its own specific properties.
In summary, we generated an overview of the auxin pathway in bamboo, which provides information for uncovering the precise roles of auxin pathway in this important species in the future.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
In mammals, DNA methylation is associated with aging. However, age‐related DNA methylation changes during phase transitions largely remain unstudied in plants. Moso bamboo (Phyllostachys ...edulis) requires a very long time to transition from the vegetative to the floral phase. To comprehensively investigate the association of DNA methylation with aging, we present here single‐base‐resolution DNA methylation profiles using both high‐throughput bisulfite sequencing and single‐molecule nanopore‐based DNA sequencing, covering the long period of vegetative growth and transition to flowering in moso bamboo. We discovered that CHH methylation gradually accumulates from vegetative to reproductive growth in a time‐dependent fashion. Differentially methylated regions, correlating with chronological aging, occurred preferentially at both transcription start sites and transcription termination sites. Genes with CG methylation changes showed an enrichment of Gene Ontology (GO) categories in ‘vegetative to reproductive phase transition of meristem’. Combining methylation data with mRNA sequencing revealed that DNA methylation in promoters, introns and exons may have different roles in regulating gene expression. Finally, circular RNA (circRNA) sequencing revealed that the flanking introns of circRNAs are hypermethylated and enriched in long terminal repeat (LTR) retrotransposons. Together, the observations in this study provide insights into the dynamic DNA methylation and circRNA landscapes, correlating with chronological age, which paves the way to study further the impact of epigenetic factors on flowering in moso bamboo.
Significance Statement
Moso bamboo requires a very long time to transition from the vegetative to the floral phase. Here, we found that the DNA methylation level varies with chronological age in moso bamboo. This study also provides insights into flanking introns of circRNAs, which are hypermethylated and enriched in LTR retrotransposons.
Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing ...technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.
We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.
AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and ...development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date.
Here, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA
, suggesting that post-transcriptional regulation might be also involved in the GA
response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA
-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition.
This study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
There are no comprehensive methods to identify N
-methyladenosine (m
A) at single-base resolution for every single transcript, which is necessary for the estimation of m
A abundance. We develop a new ...pipeline called Nanom6A for the identification and quantification of m
A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m
A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m
A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m
A.
Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated ...protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele‐aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single‐molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi‐C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein‐coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA‐Seq and PacBio single‐molecule real‐time long‐read isoform sequencing revealed highly differential alternative splicing (AS) between non‐abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high‐quality hexaploid genome and comprehensive strand‐specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
The allele‐aware chromosome‐scale assembly of the genome of the hexaploid Ma bamboo Dendrocalamus latiflorus by Pacific Biosciences Sequel sequencing and chromosome conformation capture sequencing will facilitate overexpression and CRISPRCas9 gene editing studies.
Circular RNAs (circRNAs) are a recently discovered type of non‐coding RNA derived from pre‐mRNAs. R‐loops consist of a DNA:RNA hybrid and the associated single‐stranded DNA. In Arabidopsis thaliana, ...circRNA:DNA R‐loops regulate alternative splicing (AS) of SEPALLATA3 (SEP3). However, the occurrence and functions of circRNAs and R‐loops in Populus trichocarpa are largely unexplored. Here, we performed circRNA‐enriched sequencing in the stem‐differentiating xylem (SDX) of P. trichocarpa and identified 2,742 distinct circRNAs, including circ‐CESA4, circ‐IRX7, and circ‐GUX1, which are generated from genes involved in cellulose, and hemicellulose biosynthesis, respectively. To investigate the roles of circRNAs in modulating alternative splicing (AS), we detected 7,836 AS events using PacBio Iso‐Seq and identified 634 circRNAs that overlapped with 699 AS events. Furthermore, using DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP‐seq), we identified 8,932 R‐loop peaks that overlapped with 181 circRNAs and 672 AS events. Notably, several SDX‐related circRNAs overlapped with R‐loop peaks, pointing to their possible roles in modulating AS in SDX. Indeed, overexpressing circ‐IRX7 increased the levels of R‐loop structures and decreased the frequency of intron retention in linear IRX7 transcripts. This study provides a valuable R‐loop atlas resource and uncovers the interplay between circRNAs and AS in SDX of P. trichocarpa.
Examination of circular RNAs in stem‐differentiating xylem of Populus trichocarpa by integration of multi‐omics data, including RNase R‐treated RNA sequencing, DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP‐seq), and PacBio long‐read isoform sequencing reveals circular RNAs associated with R‐loop structures in regulating alternative splicing.
Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties ...from those of normal wood (NW). Chinese fir (
) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253
full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.
Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon ...treatment with gibberellins (GAs) and auxins (1-Naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We explored the function of circRNAs, including their roles in regulating microRNA-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect microRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study gives insights into biogenesis, function, and microRNA-mediated degradation of circRNAs in moso bamboo.
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