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Guan M, Sun N, Yau SST. Geometric analysis of SARS-CoV-2 variants. Gene 2024; 909:148291. [PMID: 38417688 DOI: 10.1016/j.gene.2024.148291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 03/01/2024]
Abstract
SARS-CoV-2 as a severe respiratory disease has been prevalent around the world since its first discovery in 2019.As a single-stranded RNA virus, its high mutation rate makes its variants manifold and enables some of them to have high pathogenicity, such as Omicron variant, the most prevalent virus now. Research on the relationship of these SARS-CoV-2 variants, especially exploring their difference is a hot issue. In this study, we constructed a geometric space to represent all SARS-CoV-2 sequences of different variants. An alignment-free method: natural vector method was utilized to establish genome space. The genome space of SARS-CoV-2 was constructed based on the 24-dimensional natural vector and the appropriate metric was determined through performing phylogenetic analysises. Phylogenetic trees of different lineages constructed under the selected natural vector and metric coincided with the lineage naming standards, which means lineages with same alphabetical prefix cluster in phylogenetic trees. Furthermore, the relationships between the various GISAID clades as depicted by the natural graph primarily matched the description provided in the GISAID clade naming.The validity of our geometric space was demonstrated by these phylogenetic analysis results. So in this research, we constructed a geometry space for the genomes of the novel coronavirus SARS-CoV-2, which allows us to compare the different variants. Our geometric space is valuable for resolving the issues insides the virus.
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Affiliation(s)
- Mengcen Guan
- Department of Mathematical Sciences, Tsinghua University, Beijing, China.
| | - Nan Sun
- Department of Mathematical Sciences, Tsinghua University, Beijing, China.
| | - Stephen S-T Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China; Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
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Sun N, Zhao X, Yau SST. An efficient numerical representation of genome sequence: natural vector with covariance component. PeerJ 2022; 10:e13544. [PMID: 35729905 PMCID: PMC9206847 DOI: 10.7717/peerj.13544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background The characterization and comparison of microbial sequences, including archaea, bacteria, viruses and fungi, are very important to understand their evolutionary origin and the population relationship. Most methods are limited by the sequence length and lack of generality. The purpose of this study is to propose a general characterization method, and to study the classification and phylogeny of the existing datasets. Methods We present a new alignment-free method to represent and compare biological sequences. By adding the covariance between each two nucleotides, the new 18-dimensional natural vector successfully describes 24,250 genomic sequences and 95,542 DNA barcode sequences. The new numerical representation is used to study the classification and phylogenetic relationship of microbial sequences. Results First, the classification results validate that the six-dimensional covariance vector is necessary to characterize sequences. Then, the 18-dimensional natural vector is further used to conduct the similarity relationship between giant virus and archaea, bacteria, other viruses. The nearest distance calculation results reflect that the giant viruses are closer to bacteria in distribution of four nucleotides. The phylogenetic relationships of the three representative families, Mimiviridae, Pandoraviridae and Marsellieviridae from giant viruses are analyzed. The trees show that ten sequences of Mimiviridae are clustered with Pandoraviridae, and Mimiviridae is closer to the root of the tree than Marsellieviridae. The new developed alignment-free method can be computed very fast, which provides an effective numerical representation for the sequence of microorganisms.
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Affiliation(s)
- Nan Sun
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
| | - Xin Zhao
- Beijing Electronic Science and Technology Institute, Beijing, China
| | - Stephen S.-T. Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China,Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China
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Wan X, Tan X. A Simple Protein Evolutionary Classification Method Based on the Mutual Relations Between Protein Sequences. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200305090055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Protein is a kind of important organics in life. It is varied with its
sequences, structures and functions. Protein evolutionary classification is one of the popular
research topics in computational bioinformatics. Many studies have used protein sequence
information to classify the evolutionary relationships of proteins. As the amount of protein
sequence data increases, efficient computational tools are needed to make efficient protein
evolutionary classifications with high accuracies in the big data paradigm.
Methods:
In this study, we propose a new simple and efficient computational approach based on
the normalized mutual information rates to compute the relationship between protein sequences,
we then use the “distances” defined on the relationships to perform the evolutionary classifications
of proteins. The new method is computational efficient, model-free and unsupervised, which does
not require training data when performing classifications.
Result:
Simulation studies on various examples demonstrate the efficiency of the new method.
We use precision-recall curves to compare the efficiency of our new method with traditional
methods, results show that the new method outperforms the traditional methods in most of the
cases when performing evolutionary classifications.
Conclusion:
The new method is simple and proved to be efficient in protein evolutionary
classifications, which is useful in future evolutionary analysis particularly in the big data paradigm.
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Affiliation(s)
- Xiaogeng Wan
- Department of Mathematics, College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xinying Tan
- The Fourth Center of PLA General Hospital, Beijing, 100037, China
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Sohsah GN, Ibrahimzada AR, Ayaz H, Cakmak A. Scalable classification of organisms into a taxonomy using hierarchical supervised learners. J Bioinform Comput Biol 2020; 18:2050026. [PMID: 33125294 DOI: 10.1142/s0219720020500262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.
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Affiliation(s)
- Gihad N Sohsah
- Department of Computer Science, Istanbul Sehir University, Istanbul, Turkey
| | | | - Huzeyfe Ayaz
- Department of Computer Science, Istanbul Sehir University, Istanbul, Turkey
| | - Ali Cakmak
- Department of Computer Engineering, Istanbul Technical University, Istanbul, Turkey
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Doilom M, Guo JW, Phookamsak R, Mortimer PE, Karunarathna SC, Dong W, Liao CF, Yan K, Pem D, Suwannarach N, Promputtha I, Lumyong S, Xu JC. Screening of Phosphate-Solubilizing Fungi From Air and Soil in Yunnan, China: Four Novel Species in Aspergillus, Gongronella, Penicillium, and Talaromyces. Front Microbiol 2020; 11:585215. [PMID: 33123114 PMCID: PMC7574596 DOI: 10.3389/fmicb.2020.585215] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/11/2020] [Indexed: 11/25/2022] Open
Abstract
Phosphate-solubilizing fungi (PSF) play an important role in increasing the bioavailability of phosphorus in soils for plants. Thirteen fungal strains, one collected from air and 12 from soil, were screened and described here in detail. These fungal strains were tested for their ability to solubilize tricalcium phosphate (TCP) on both solid and liquid Pikovskaya (PVK) media in vitro. The airborne fungal strain KUMCC 18-0196 (Aspergillus hydei sp. nov.) showed the most significant phosphate solubilizing activity on a solid PVK medium with the solubilization index (SI) (2.58 ± 0.04 cm) and the highest solubilized phosphates (1523.33 ± 47.87 μg/mL) on a liquid PVK medium. To the best of our knowledge, A. hydei sp. nov. is the first phosphate-solubilizing fungus reported from air. We also provide the identification especially for Aspergillus, Penicillium and Talaromyces, generally reported as PSF. It is important to not only screen for PSF but also identify species properly so that researchers have a clearer taxonomic picture for identifying potential taxa for future plant growth-promoting applications. Herein, A. hydei (section Nigri), Gongronella hydei, Penicillium soli (section Lanata-Divaricata) and Talaromyces yunnanensis (section Talaromyces) are fully described and introduced as new to science. These four new species are identified based on both morphological characteristics and multigene phylogenetic analyses, including the genealogical concordance phylogenetic species recognition method where necessary. Penicillium austrosinense is considered to be a synonym of P. guaibinense.
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Affiliation(s)
- Mingkwan Doilom
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jian-Wei Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
| | - Rungtiwa Phookamsak
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Peter E. Mortimer
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Samantha C. Karunarathna
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
| | - Wei Dong
- Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Chun-Fang Liao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
| | - Kai Yan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Dhandevi Pem
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Jian-Chu Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Honghe Innovation Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, East and Central Asia, Kunming, China
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