Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)

• 作者: Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan Yubang Gao Hangxiao Zhang Lianfeng Gu
• 来源期刊: 植物学报（英文版）
• 年，卷（期）: 2022,（3）
• 所属期刊栏目: New Resources
• 页码范围: 649-670
• 页数: 22页
• 语种: 英文

摘要

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly in-terspaced 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 con-formation capture sequencing (Hi-C). Repetitive sequences comprised 52.65％ of the D. latiflorus genome. We annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome se-quencing 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, sug-gesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid ge-nome and comprehensive strand-specific tran-scriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.