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ABSTRACT: Transcriptome between WT and STTM156 in Dendrocalamus latiflorus Munro

PROVIDER: PRJNA987326 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25016619_1.fastq.gz	Fastqsanger.gz
	SRR25016619_2.fastq.gz	Fastqsanger.gz
	SRR25016620_1.fastq.gz	Fastqsanger.gz
	SRR25016620_2.fastq.gz	Fastqsanger.gz
	SRR25016621_1.fastq.gz	Fastqsanger.gz

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Chromosome-scale assembly of hexaploid genome of Ma Bamboo (Dendrocalamus latiflorus Munro)

Project description:Dendrocalamus latiflorus Munro (D. latiflorus) is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and CRISPR-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 (SMRT) long-read isoform sequencing (Iso-Seq) 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.

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Project description:The economically important bamboo species Dendrocalamus latiflorus Munro (D. latiflorus) exhibits highly susceptible to Bamboo mosaic virus (BaMV), resulting in severe growth and development impairment. However, the proteomic profiles, transcript processing dynamics, and their coordinated post-transcriptional regulation during bamboo-virus interactions remain uncharacterized. Tandem mass tag (TMT)-based quantitative proteomic revealed suppression of photosynthesis-related proteins and upregulation of protein synthesis and degradation, antioxidant within D. latiflorus during BaMV infection. Moreover, the APR1 protein serviced as a regulatory hub for connecting sulfur metabolism, antioxidant, and photosynthesis. Integration of nanopore direct RNA sequencing (DRS) data revealed reduced D. latiflorus full-length read ratios, consequently attenuating transcriptome and proteome correlation. BaMV infected bamboos presented preferential usage of distal poly(A) site and lengthened poly(A) tail lengths (PALs) of pathogenesis-related (PR) genes. Epitranscriptome analysis showed increased N6-methyladenosine (m6A) ratios in POR (chlorophyll synthesis) and NCED1 (abscisic acid synthesis), which coupled with reduced transcriptional levels. In total, 122 potential m6A modification sites were found in BaMV, with AAACA representing the predominant consensus motif. Collectively, these results offer insights into post-transcriptional regulation networks during bamboo-BaMV interactions.

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