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琉球群岛芋头((L.) Schott)的一个水稻品种台芋叶绿体基因组测序。

Sequencing of the chloroplast genome of Taimo, a paddy cultivar of Taro ( (L.) Schott) in the Ryukyu Archipelago.

作者信息

Takaesu Reina, Kinjo Yukihiro, Clitheroe Crystal-Leigh, Sunagawa Haruki, Bourguignon Thomas, Saitoh Seikoh

机构信息

Department of Regional Economics and Environmental Policy, Okinawa International University, Ginowan, Japan.

Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya, Yokohama, Japan.

出版信息

Mitochondrial DNA B Resour. 2025 May 20;10(6):508-512. doi: 10.1080/23802359.2025.2505789. eCollection 2025.

DOI:10.1080/23802359.2025.2505789
PMID:40400642
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12093797/
Abstract

Taimo is a paddy cultivar of Taro ( (L.) Schott) that is traditionally consumed in the Ryukyu Archipelago, Japan. Its origin remains unknown, although it has been identified as belonging to a haplotype commonly found in tropical and subtropical regions. However, previously developed genetic markers were insufficient to resolve the genetic relationships among cultivars that share the same haplotype. To address this limitation, we sequenced the complete chloroplast genome of cv. Taimo. The comparison of the obtained sequence with the currently published complete and partial chloroplast genomes revealed that cv. Taimo is most closely related to the paddy cultivar Lipu from southern mainland China. These findings suggest that the ancestors of cv. Taimo were introduced to the Ryukyus from China.

摘要

台芋是一种芋头((L.) Schott)的水稻品种,传统上在日本琉球群岛食用。其起源尚不清楚,尽管它已被鉴定为属于热带和亚热带地区常见的单倍型。然而,先前开发的遗传标记不足以解析具有相同单倍型的品种之间的遗传关系。为了解决这一限制,我们对台芋品种的完整叶绿体基因组进行了测序。将获得的序列与目前已发表的完整和部分叶绿体基因组进行比较,结果表明台芋品种与中国南部大陆的水稻品种荔浦关系最为密切。这些发现表明,台芋品种的祖先从中国被引入到琉球。

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本文引用的文献

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Genomics. 2021 Jan;113(1 Pt 1):183-192. doi: 10.1016/j.ygeno.2020.12.016. Epub 2020 Dec 14.
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Evolutionary origins of taro () in Southeast Asia.芋头()在东南亚的进化起源。 (注:原文括号里内容缺失,翻译只能按现有内容进行)
Ecol Evol. 2020 Nov 2;10(23):13530-13543. doi: 10.1002/ece3.6958. eCollection 2020 Dec.
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Using SPAdes De Novo Assembler.使用 SPAdes 从头组装。
Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102.
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GSAlign: an efficient sequence alignment tool for intra-species genomes.GSAlign:一种用于种内基因组的高效序列比对工具。
BMC Genomics. 2020 Feb 24;21(1):182. doi: 10.1186/s12864-020-6569-1.
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CPGAVAS2, an integrated plastome sequence annotator and analyzer.CPGAVAS2,一个集成的质体基因组序列注释和分析器。
Nucleic Acids Res. 2019 Jul 2;47(W1):W65-W73. doi: 10.1093/nar/gkz345.
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OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.细胞器基因组绘图 (OGDRAW) 版本 1.3.1:用于细胞器基因组图形可视化的扩展工具包。
Nucleic Acids Res. 2019 Jul 2;47(W1):W59-W64. doi: 10.1093/nar/gkz238.
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Nucleic Acids Res. 2016 Jul 8;44(W1):W232-5. doi: 10.1093/nar/gkw256. Epub 2016 Apr 15.
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Mol Ecol Resour. 2013 Sep;13(5):929-37. doi: 10.1111/1755-0998.12128. Epub 2013 May 30.