Sun Jingjing, Chen Yuancai, Wei Yizhuo, Zhang Kaihui, Fu Yin, Yan Zi, Zhu Xingyu, Zhang Sumei, Zhang Longxian, Li Junqiang
College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, 450046, China.
Sci Data. 2025 Jul 1;12(1):1079. doi: 10.1038/s41597-025-05405-x.
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.
十二指肠贾第虫是一种引起重要人畜共患病关注的原生动物寄生虫，据估计，全球每年约有2.8亿人感染。目前，十二指肠贾第虫的基因组测序主要依赖于体外无菌克隆；然而，对于不可培养或难以培养的微生物，获取足够的DNA进行全基因组测序是一项巨大的挑战。在本研究中，我们使用单细胞分选技术分离出10个十二指肠贾第虫滋养体，随后提取全基因组DNA并通过多重置换扩增（MDA）进行扩增。通过长读长测序（牛津纳米孔技术公司和太平洋生物科学公司）对十二指肠贾第虫DNA进行测序，并使用三种主要的组装工具（Canu、MECAT2和RagTag）对测序数据进行组装。结果，成功组装出十二指肠贾第虫的染色体水平基因组（A1群分离株g12a2），基因组总大小为11.1 Mbp，有5个重叠群，N50值为3.1 Mbp。本研究从10个滋养体群体中实现了十二指肠贾第虫染色体水平的基因组测序和组装，这有助于原生动物单细胞基因组学研究。
