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ABSTRACT: Transcriptome sequencing in Dendrocalamus latiflorus

PROVIDER: PRJNA766349 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16093295_1.fastq.gz	Fastqsanger.gz
	SRR16093295_2.fastq.gz	Fastqsanger.gz
	SRR16093296_1.fastq.gz	Fastqsanger.gz
	SRR16093296_2.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.

2021-11-20 | GSE155494 | GEO

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