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Title: Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon
Authors: Sato, Mitsuhiko P
Iwakami, Satoshi  kyouindb  KAKEN_id  orcid (unconfirmed)
Fukunishi, Kanade
Sugiura, Kai
Yasuda, Kentaro
Isobe, Sachiko
Shirasawa, Kenta
Author's alias: 佐藤, 光彦
岩上, 哲史
福西, 詩奏
杉浦, 快
保田, 謙太郎
磯部, 祥子
白澤, 健太
Keywords: genome assembly
Issue Date: Oct-2023
Publisher: Oxford University Press (OUP)
Kazusa DNA Research Institute
Journal title: DNA Research
Volume: 30
Issue: 5
Thesis number: dsad023
Abstract: Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32, 337, and 30, 889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.
Description: タイヌビエのゲノムを高精度解読 --除草剤に抵抗性を持つ水田の雑草タイヌビエの高精度ゲノム解読に成功--. 京都大学プレスリリース. 2023-11-07.
Rights: © The Author(s) 2023. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI(Published Version): 10.1093/dnares/dsad023
PubMed ID: 37943179
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