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 con?formation 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 se?quencing using RNA‐Seq and PacBio single‐molecule real‐time long‐read isoform sequencingrevealed highly differential alternative splicing (AS)between non‐abortive and abortive shoots, sug?gesting that AS regulates the abortion rate ofbamboo shoots. This high‐quality hexaploid ge?nome and comprehensive strand‐specific tran?scriptome datasets for this Poaceae familymember will pave the way for bamboo researchusing D. latiflorus as a model species.