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病毒准种全长一致性序列的精确组装。

Accurate assembly of full-length consensus for viral quasispecies.

作者信息

Tian Jia, Gao Ziyu, Li Minghao, Bao Ergude, Zhao Jin

机构信息

College of Computer Science and Technology, Qingdao University, Qingdao, China.

School of Software Engineering, Beijing Jiaotong University, Beijing, China.

出版信息

BMC Bioinformatics. 2025 Feb 1;26(1):36. doi: 10.1186/s12859-025-06045-z.

DOI:10.1186/s12859-025-06045-z
PMID:39893441
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11787740/
Abstract

BACKGROUND

Viruses can inhabit their hosts in the form of an ensemble of various mutant strains. Reconstructing a robust consensus representation for these diverse mutant strains is essential for recognizing the genetic variations among strains and delving into aspects like virulence, pathogenesis, and selecting therapies. Virus genomes are typically small, often composed of only a few thousand to several hundred thousand nucleotides. While constructing a high-quality consensus of virus strains might seem feasible, most current assemblers only generated fragmented contigs. It's important to emphasize the significance of assembling a single full-length consensus contig, as it's vital for identifying genetic diversity and estimating strain abundance accurately.

RESULTS

In this paper, we developed FC-Virus, a de novo genome assembly strategy specifically targeting highly diverse viral populations. FC-Virus first identifies the k-mers that are common across most viral strains, and then uses these k-mers as a backbone to build a full-length consensus sequence covering the entire genome. We benchmark FC-Virus against state-of-the-art genome assemblers.

CONCLUSION

Experimental results confirm that FC-Virus can construct a single, accurate full-length consensus, whereas other assemblers only manage to produce fragmented contigs. FC-Virus is freely available at https://github.com/qdu-bioinfo/FC-Virus.git .

摘要

背景

病毒能够以多种突变株集合的形式寄生于宿主。为这些多样的突变株构建一个可靠的一致表示对于识别菌株间的遗传变异以及深入研究毒力、发病机制和选择治疗方法等方面至关重要。病毒基因组通常较小，往往仅由几千到几十万核苷酸组成。虽然构建高质量的病毒株一致序列看似可行，但目前大多数组装工具仅生成片段化的重叠群。强调组装单个全长一致重叠群的重要性很有必要，因为这对于准确识别遗传多样性和估计菌株丰度至关重要。

结果

在本文中，我们开发了FC-Virus，这是一种专门针对高度多样化病毒群体的从头基因组组装策略。FC-Virus首先识别大多数病毒株中常见的k-mer，然后将这些k-mer用作主干来构建覆盖整个基因组的全长一致序列。我们将FC-Virus与最先进的基因组组装工具进行了基准测试。

结论

实验结果证实，FC-Virus能够构建单一、准确的全长一致序列，而其他组装工具只能生成片段化的重叠群。FC-Virus可在https://github.com/qdu-bioinfo/FC-Virus.git上免费获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/e68ceabd3c20/12859_2025_6045_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/a568bdc83d0e/12859_2025_6045_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/37da2e9346aa/12859_2025_6045_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/ea6ef1e49126/12859_2025_6045_Figa_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/8f12e232f042/12859_2025_6045_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/ae2e0648d639/12859_2025_6045_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/9e1291ba9f5f/12859_2025_6045_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/af892e9fcfef/12859_2025_6045_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/e68ceabd3c20/12859_2025_6045_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/a568bdc83d0e/12859_2025_6045_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/37da2e9346aa/12859_2025_6045_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/ea6ef1e49126/12859_2025_6045_Figa_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/8f12e232f042/12859_2025_6045_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/ae2e0648d639/12859_2025_6045_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/9e1291ba9f5f/12859_2025_6045_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/af892e9fcfef/12859_2025_6045_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b49f/11787740/e68ceabd3c20/12859_2025_6045_Fig7_HTML.jpg

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