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<p><i>Giardia duodenalis</i>, a protozoan parasite of important zoonotic concern, is estimated to cause approximately 280 million human infections annually worldwide. Currently, genome sequencing of <i>G. duodenalis</i> mainly relies on <i>in vitro</i> axenic clones; however, for non-culturable or hard-to-cultivate microorganisms, obtaining sufficient DNA for whole-genome sequencing poses a great challenge. In this study, we isolated ten <i>G. duodenalis</i> trophozoites using single-cell selection technology, followed by the extraction of whole-genome DNA and its amplification via multiple displacement amplification (MDA). The <i>G. duodenalis</i> DNA was sequenced by long-read sequencing (Oxford Nanopore Technologies and Pacific Biosciences), and three main assembly tools (Canu, MECAT2, and RagTag) were used to assemble the sequenced data. As a result, a chromosome-scale genome of <i>G. duodenalis</i> was successfully assembled (assemblage A1 isolate g12a2), with a total genome size of 11.1 Mbp, five contigs, and an N50 value of 3.1 Mbp. This study achieved a chromosome-scale <i>G. duodenalis</i> genome sequencing and assembly from groups of 10 trophozoites, which facilitates protozoan single cell genomics research.</p>

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A chromosome-scale genome assembly of Giardia duodenalis by long-read sequencing of ten trophozoites

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月1日

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  • Jingjing Sun,
  • Yuancai Chen,
  • Yizhuo Wei,
  • Kaihui Zhang,
  • Yin Fu,
  • Zi Yan,
  • Xingyu Zhu,
  • Sumei Zhang,
  • Longxian Zhang,
  • Junqiang Li

摘要

Giardia duodenalis, a protozoan parasite of important zoonotic concern, is estimated to cause approximately 280 million human infections annually worldwide. Currently, genome sequencing of G. duodenalis mainly relies on in vitro axenic clones; however, for non-culturable or hard-to-cultivate microorganisms, obtaining sufficient DNA for whole-genome sequencing poses a great challenge. In this study, we isolated ten G. duodenalis trophozoites using single-cell selection technology, followed by the extraction of whole-genome DNA and its amplification via multiple displacement amplification (MDA). The G. duodenalis DNA was sequenced by long-read sequencing (Oxford Nanopore Technologies and Pacific Biosciences), and three main assembly tools (Canu, MECAT2, and RagTag) were used to assemble the sequenced data. As a result, a chromosome-scale genome of G. duodenalis was successfully assembled (assemblage A1 isolate g12a2), with a total genome size of 11.1 Mbp, five contigs, and an N50 value of 3.1 Mbp. This study achieved a chromosome-scale G. duodenalis genome sequencing and assembly from groups of 10 trophozoites, which facilitates protozoan single cell genomics research.