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Dendrocalamus latiflorus Munro (D. latiflorus) is a woody clumping bamboo, which presented fast growth in shoot. Both overexpression and CRISPR-Cas9 gene editing are available to elucidate gene function in D. latiflorus. Thus, D. latiflorus has a potential to be a model bamboo to investigate the molecular mechanism of bamboo flower and fast growth. However, the genome sequence was unreported due to the challenging of polyploid (2n=6X=72) and big genome size of of D. latiflorus. Here, we reported 2621.24 Mb chromosome-scale assembly of high-quality reference genome of hexaploid D. latiflorus with N50 for contig and scaffold of 2.57Mb and 4.5Mb, respectively. The largest scaffold was 21.73 Mb using ultra-long PacBio reads by Pacific Biosciences Sequel sequencing. Combination with chromosome conformation capture sequencing (Hi-C) genome of D. latiflorus was anchored into chromosome-scale assembly with the largest chromosome-length scaffolds being 61 Mb, which represented the biggest genome in major bamboo lineages. Furthermore, a total of 135,866 protein-coding genes in the D. latiflorus genome were annotated using transcriptome, with an average transcript length of 3,952 bp and a mean of 4.52 exons per gene. Finally, we showed that 54.26% genome of D. latiflorus were classified as repeat sequence. In summary, this study generated a hexaploid genome in high-quality chromosome level for Poaceae family, which will provide great convenience for bamboo research to use D. latiflorus as a model species in future.


News:

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis) | September 2018

Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies.Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy.

Allele‐aware chromosome‐scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro) | March 2022

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), representing the largest genome of a major bamboo species.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos | March 2022

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid).


Refference

  • Zhao H, Gao Z, Wang L, et al. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. Gigascience, 2018, 7(10): giy115.
  • Guo Z H, Ma P F, Yang G Q, et al. Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos[J]. Molecular plant, 2019, 12(10): 1353-1365.
  • Zheng Y, Yang D, Rong J, et al. Allele‐aware chromosome‐scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro)[J]. Journal of Integrative Plant Biology, 2022.
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