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

第一作者：Yushan Zheng

第一单位：福建农林大学

通讯作者：Lianfeng Gu

 Abstarct 

背景回顾：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. 

麻竹（Dendrocalamus latiflorus）是一种生长迅速的木本丛生竹。已经成功构建了适合麻竹的遗传转化和CRISPR/Cas9基因组编辑体系，能够通过反向遗传方法对麻竹进行基因功能鉴定。因此，麻竹有潜力成为一种模式竹种。

提出问题：However, the genome sequence of D. latiflorushas remained unreported due to its polyploidy and large genome size. 

然而，由于麻竹为多倍体且基因组较大，目前尚未有其基因组序列的报道。

主要研究： 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. 

本文中，作者对麻竹进行了全基因组测序，并通过组装获得了三个亚基因组（AABBCC），代表一个主要竹种的最大基因组。

结果1-基因组组装、注释：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. 

作者通过对六倍体麻竹的PacBio单分子测序和染色体构象捕获测序Hi-C的数据，组装获得了70个等位染色体（2737Mb）。麻竹基因组中，重复序列占了约52.65%。作者根据对八个不同麻竹组织的转录组数据，共注释了麻竹基因组中135231个蛋白质编码基因。

结果2-麻竹退笋：Transcriptome sequencing 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, suggesting that AS regulates the abortion rate of bamboo shoots. 

通过RNA-Seq和PacBio三代全长转录本测序，作者发现正常发育的麻竹笋和退笋之间存在高度差异的可变剪接，表明可变剪切调节了麻竹退笋率。

结论：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.

本文所报道的高质量的六倍体麻竹基因组以及该物种全面的链特异性转录组数据集，将为以麻竹为模式竹种的研究铺平道路。

** 顾连峰 **

doi: https://doi.org/10.1111/jipb.13217

Journal: Journal of Integrative Plant Biology

First Published:  January 06, 2022