Application of co-barcoding single tube long fragment read technology in genome research

doi:10.3877/cma.j.issn.2095-1221.2022.02.010

Abstract

Abstract:

Single tube long fragment read (stLFR) refers to an unseparated long fragment reading technique, which can attach to the read sequencing fragments from the same long DNA molecule with the same molecular label. The library can be prepared by this technology and it may generate short read length (200 ~ 1 000 bp) fragments for sequencing. After co-barcoding analysis, it can splice long fragment sequences. Therefore, it is capable of long fragment analysis similarly to the third-generation sequencing in theory. At present, the technology is mainly used to assemble target samples, and studies have been reported in humans, plants, animals, microorganisms, and so on. However, the technology has not been fully utilized. Therefore, the review of co-barcoding stLFR can provide references for solving the functional study of long genome fragments.

Key words: Single tube long fragment read, Gene assembly, Chromosomal structural variation, scRNA-seq

Shuai Kou, Zhiping Jin, Yining Huang, Lianming Liao. Application of co-barcoding single tube long fragment read technology in genome research[J]. Chinese Journal of Cell and Stem Cell(Electronic Edition), 2022, 12(02): 121-126.

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References 37

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物种名称	Contig N50	Scaffold N50	基因功能注释	基因组完整性评估	测序深度
有袋类负鼠	56.91 kb	683.53 Mb	83.90﹪	88.10﹪	100x
圆斑星鲽	79.80 kb	23.80 Mb	95.00﹪	97.20﹪	214.72x
GM12878细胞系	99.78 kb	29.02 Mb	—	91.00﹪	44x
澳洲坚果^[19]	35.60 kb	3.54 Mb	—	88.30﹪	96x
草地贪叶蛾	91.97 kb	0.51 Mb	85.48﹪	95.00﹪	205x
驼背豚	1.78 Mb	15.80 Mb	90.70﹪	95.70﹪	—
冰川红杆菌^[22]	2.80 Mb	4.60 Mb	99.97﹪	99.97﹪	500x
刺鲀^[23]	70.84 kb	6.10 Mb	87.72﹪	95.70﹪	219.8x
湄公河虎鲈^[24]	171.23 kb	9.73 Mb	—	95.19﹪	121x

物种名称	Contig N50	Scaffold N50	基因功能注释	基因组完整性评估	测序深度
有袋类负鼠	56.91 kb	683.53 Mb	83.90﹪	88.10﹪	100x
圆斑星鲽	79.80 kb	23.80 Mb	95.00﹪	97.20﹪	214.72x
GM12878细胞系	99.78 kb	29.02 Mb	—	91.00﹪	44x
澳洲坚果^[19]	35.60 kb	3.54 Mb	—	88.30﹪	96x
草地贪叶蛾	91.97 kb	0.51 Mb	85.48﹪	95.00﹪	205x
驼背豚	1.78 Mb	15.80 Mb	90.70﹪	95.70﹪	—
冰川红杆菌^[22]	2.80 Mb	4.60 Mb	99.97﹪	99.97﹪	500x
刺鲀^[23]	70.84 kb	6.10 Mb	87.72﹪	95.70﹪	219.8x
湄公河虎鲈^[24]	171.23 kb	9.73 Mb	—	95.19﹪	121x

	NGS	ONT-nanopore	PacBio-SMRT	MGI-stLFR	Nanopore+ SMRT	Nanopore+ tLFR	SMRT+ tLFR
覆盖率评估	最低	中等	较高	较高	> 90﹪	> 90﹪	> 90﹪
错误率评估	最低	最高	略高于NGS	略高于NGS	中等	略高于NGS	略高于NGS
样本获得成本	最低	略高于NGS	最高	较高	—	—	—
建库成本评估	最低	较高	较高	略高于NGS	—	—	—
测序成本评估	最低	最高	最高	与NGS相当	—	—	—

	NGS	ONT-nanopore	PacBio-SMRT	MGI-stLFR	Nanopore+ SMRT	Nanopore+ tLFR	SMRT+ tLFR
覆盖率评估	最低	中等	较高	较高	> 90﹪	> 90﹪	> 90﹪
错误率评估	最低	最高	略高于NGS	略高于NGS	中等	略高于NGS	略高于NGS
样本获得成本	最低	略高于NGS	最高	较高	—	—	—
建库成本评估	最低	较高	较高	略高于NGS	—	—	—
测序成本评估	最低	最高	最高	与NGS相当	—	—	—

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