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 

机构地区：[1]College of Forestry,Fujian Agriculture and Forestry University,Fuzhou 350002,China [2]College of Landscape Architecture,Fujian Agriculture and Forestry University,Fuzhou 350002,China [3]Basic Forestry and Proteomics Research Center,College of Forestry,Fujian Provincial Key Laboratory of Haixia Applied PlantSystems Biology,Fujian Agriculture and Forestry University,Fuzhou 350002,China

出　　处：《Journal of Integrative Plant Biology》2022年第3期649-670,共22页植物学报（英文版）

基　　金：supported by the National Key Research and Development Program of China(2018YFD0600104);the National Natural Science Foundation of China Grant(31971734);the Natural Science Foundation of Fujian Province(Grant No.2021J02027);the Distinguished Young Scholar Program of Fujian Agriculture and Forestry University(Grant No.xjq202017);the Technological Innovation Team at the University of Fujian province;the Forestry Peak Discipline Construction Project from Fujian Agriculture and Forestry University。

摘　　要：Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth.Both genetic transformation and clustered regularly interspaced 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),representingthe largest genome of a major bamboo species.We assembled 70 allelic chromosomes(2,737 Mb)for hexaploid D.latiflorus using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation 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 sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing 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.

关 键 词：alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing 

分 类 号：S795.5[农业科学—林木遗传育种]