Allele‐aware chromosome‐scale assembly of theallopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

Dendrocalamus latiflorus Munro is a woodyclumping bamboo with rapid shoot growth. Bothgenetic transformation and clustered regularly in terspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) gene editingtechniques are available for D. latiflorus, enablingreverse genetic approaches. Thus, D. latiflorushas the potential to be a model bamboo species.However, the genome sequence of D. latiflorushas remained unreported due to its polyploidyand large genome size. Here, we sequenced theD. latiflorus genome and assembled it into threeallele‐aware subgenomes (AABBCC), representingthe 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). Repetitivesequences comprised 52.65% of the D. latiflorusgenome. We annotated 135 231 protein‐codinggenes in the genome based on transcriptomesfrom eight different tissues. Transcriptome sequencing using RNA‐Seq and PacBio single‐molecule real‐time long‐read isoform sequencingrevealed highly differential alternative splicing (AS)between non‐abortive and abortive shoots, suggesting that AS regulates the abortion rate ofb amboo shoots. This high‐quality hexaploid genome and comprehensive strand‐specific transcriptome datasets for this Poaceae familymember will pave the way for bamboo researchusing D. latiflorus as a model species.. Please cite following reference if you use this dataset in your study:Zheng, Y., Yang, D., Rong, J., Chen, L., Zhu, Q., He, T., ... &amp; Gu, L. (2022). Allele‐aware chromosome‐scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro). <i>Journal of Integrative Plant Biology</i>, <i>64</i>(3), 649-670.All suggestions are welcome to [e-mail]

麻竹（Dendrocalamus latiflorus Munro）是一种木质丛生竹，笋芽生长迅速。目前遗传转化技术与成簇规律间隔短回文重复序列（clustered regularly interspaced short palindromic repeats, CRISPR）/CRISPR相关蛋白9（Cas9）基因编辑技术均可应用于麻竹，可为反向遗传学研究提供技术支撑。因此，麻竹具备成为竹类模式物种的潜力。
然而，由于其多倍体特性与庞大的基因组规模，麻竹的基因组序列至今尚未被公开报道。
本研究对麻竹基因组进行测序，并将其组装为3个等位基因识别型亚基因组（AABBCC），该组装结果对应主要竹类物种中规模最大的基因组。针对六倍体麻竹，本研究结合太平洋生物科学（Pacific Biosciences, PacBio）Sequel平台的单分子测序技术与染色体构象捕获测序（Hi-C）技术，组装得到70条等位染色体，基因组总长度达2737 Mb。重复序列占麻竹基因组的52.65%。
本研究基于8种不同组织的转录组数据，对该基因组注释得到135231个蛋白质编码基因。通过RNA测序（RNA-Seq）与PacBio单分子实时长读长异构体测序开展转录组分析，本研究发现正常发育笋与败育笋之间存在显著差异的可变剪接（alternative splicing, AS）事件，提示可变剪接可调控竹笋败育率。
这份高质量的六倍体基因组与针对该禾本科（Poaceae）物种的全面链特异性转录组数据集，将为以麻竹作为模式物种开展竹类研究奠定基础。若您在研究中使用本数据集，请引用以下文献：Zheng Y, Yang D, Rong J, Chen L, Zhu Q, He T, 等 (2022) 六倍体麻竹（Dendrocalamus latiflorus Munro）异源多倍体基因组的等位基因识别型染色体规模组装. 《整合植物生物学杂志》（Journal of Integrative Plant Biology）, 64(3): 649-670。欢迎致信[e-mail]提出任何建议。