scholarly journals Constructing phylogenetic relationship based on the independent selection law of genome sequences

2021 ◽  
Author(s):  
Xiaolong Li ◽  
Hong Li ◽  
Zhenhua Yang ◽  
Zefeng Zhang
Keyword(s):  
Phylogenetic Relationship ◽  
Relative Frequency ◽  
Phylogenetic Trees ◽  
Sequence Evolution ◽  
Genome Sequences ◽  
Insect Genome ◽  
High Profile ◽  
Genome Level ◽  
The Given ◽  
Evolution Of Genomes

Abstract Background: Exploring the composition and evolution regularity of genome sequences and constructing phylogenetic relationship by alignment-free method in genome level are high-profile topics. Our previous researches discovered the CG and TA independent selection laws existed in genome sequences by analysis on the spectral features of 8-mer subsets of 920 eukaryote and prokaryote genomes. We found that the evolution state of genomes is determined by the intensity of the two independent selections and the degree of the mutual inhibition between them. Results: In this study, the two independent selection patterns of 22 primate and 28 insect genome sequences were analyzed further. The two complete 8-mer motif sets containing CG or TA dinucleotide and their feature of relative frequency are proposed. We found that the two 8-mer sets and their feature are related directly to sequence evolution of genomes. According to the relative frequency of two 8-mer sets, phylogenetic trees were constructed respectively for the given primate and insect genomes. Through analysis and comparison, we found that our phylogenetic trees are more consistent with the known conclusions. Conclusions: The two kinds of phylogenetic relationships constructed by CG 8-mer set and TA 8-mer set are similar in insect genomes, but the phylogenetic relationship constructed by CG 8-mer set reflect the evolution state of genomes in current age and phylogenetic relationship constructed by TA 8-mer set reflect the evolution state of genomes in a slight earlier period. We thought it is the result that the TA independent selection is repressed by the CG independent selection in the process of genome evolution. Our study provides a theoretical approach to construct more objective evolution relationships in genome level.

scholarly journals Constructing phylogenetic relationship based on the independent selection law of genome sequences

2021 ◽  
Author(s):  
Xiaolong Li ◽  
Hong Li ◽  
Zhenhua Yang ◽  
Zefeng Zhang
Keyword(s):  
Phylogenetic Relationship ◽  
Relative Frequency ◽  
Phylogenetic Trees ◽  
Sequence Evolution ◽  
Genome Sequences ◽  
Insect Genome ◽  
High Profile ◽  
Genome Level ◽  
The Given ◽  
Evolution Of Genomes

Exploring the composition and evolution regularity of genome sequences and constructing phylogenetic relationship by alignment-free method in genome level are high-profile topics. Our previous researches discovered the CG and TA independent selection laws existed in genome sequences by analysis on the spectral features of 8-mer subsets of 920 eukaryote and prokaryote genomes. We found that the evolution state of genomes is determined by the intensity of the two independent selections and the degree of the mutual inhibition between them. In this study, the two independent selection patterns of 22 primate and 28 insect genome sequences were analyzed further. The two complete 8-mer motif sets containing CG or TA dinucleotide and their feature of relative frequency are proposed. We found that the two 8-mer sets and their feature are related directly to sequence evolution of genomes. According to the relative frequency of two 8-mer sets, phylogenetic trees were constructed respectively for the given primate and insect genomes. Through analysis and comparison, we found that our phylogenetic trees are more consistent with the known conclusions. The two kinds of phylogenetic relationships constructed by CG 8-mer set and TA 8-mer set are similar in insect genomes, but the phylogenetic relationship constructed by CG 8-mer set reflect the evolution state of genomes in current age and phylogenetic relationship constructed by TA 8-mer set reflect the evolution state of genomes in a slight earlier period. We thought it is the result that the TA independent selection is repressed by the CG independent selection in the process of genome evolution. Our study provides a theoretical approach to construct more objective evolution relationships in genome level.

scholarly journals Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 764
Author(s):  
Bohu Pan ◽  
Zuowei Ji ◽  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Jie Liu ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Host Age ◽  
Hierarchical Clustering Analysis ◽  
Genome Sequences ◽  
Geographic Patterns ◽  
Rapid Spread ◽  
Pairwise Sequence Similarity ◽  
Sequence Similarity Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.

scholarly journals Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs

2020 ◽  
Vol 11 ◽  
Author(s):  
Huimin Liu ◽  
Zhibin Shi ◽  
Chunguo Liu ◽  
Pengfei Wang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Pseudorabies Virus ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Full Genome Sequence ◽  
Genome Sequences ◽  
Protein Coding ◽  
One Step ◽  
Human Infections ◽  
Full Length Genome

Pseudorabies viruses (PRVs) pose a great threat to the pig industry of many countries around the world. Human infections with PRV have also been reported occasionally in China. Therefore, understanding the epidemiology and evolution of PRVs is of great importance for disease control in the pig populations and humans as well. In this study, we isolated a PRV designated HLJ-2013 from PRV-positive samples that had been collected in Heilongjiang, China, in 2013. The full genome sequence of the virus was determined to be ∼143 kbp in length using high-throughput sequencing. The genomic sequence identities between this isolate and 21 other previous PRV isolates ranged from 92.4% (with Bartha) to 97.3% (with SC). Phylogenetic analysis based on the full-length genome sequences revealed that PRV HLJ-2013 clustered together with all the Chinese strains in one group belonging to Genotype II, but this virus occurred phylogenetically earlier than all the other Chinese PRV strains. Phylogenetic trees based on both protein-coding genes and non-coding regions revealed that HLJ-2013 probably obtained its genome sequences from three origins: a yet unknown parent virus, the European viruses, and the same ancestor of all Chinese PRVs. Recombination analysis showed that HLJ-2013-like virus possibly donated the main framework of the genome of the Chinese PRVs. HLJ-2013 exhibited cytopathic and growth characteristics similar to that of the Chinese PRV strains SC and HeN1, but its pathogenicity in mice was higher than that of SC and lower than that of HeN1. The identification of HLJ-2013 takes us one step closer to understanding the origin of PRVs in China and provides new knowledge about the evolution of PRVs worldwide.

Phylogenetic relationship of potato CAT1 and CAT2 genes, their differential expression in non-photosynthetic organs and during leaf development, and their association with different cellular processes

2006 ◽  
Vol 33 (7) ◽  
pp. 639 ◽  
Author(s):  
Isabel Santos ◽  
Helena Pires ◽  
José M. Almeida ◽  
Fernanda Fidalgo ◽  
Ana Confraria ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Activity Patterns ◽  
Developmental Phase ◽  
High Identity ◽  
Solanaceous Species ◽  
Cdna Sequences ◽  
Cellular Processes ◽  
Relationship Of ◽  
Expression And Activity

Plants contain multiple forms of catalase (CAT) and their specific functions remain uncertain. We cloned two potato cDNAs corresponding to CAT1 and CAT2 genes, analysed their phylogenetic relationship, and studied their expression and activity in different organs to gain clues to their functions. Phylogenetic trees and the alignment of CAT cDNA sequences provided evidence that CAT1 and CAT2 genes have high identity to catalases of other solanaceous species, but are not phylogenetically closely related to one another, which contradicts the phylogenetic closeness ascribed to these genes. Northern blot analyses revealed that expression of CAT genes is controlled by leaf developmental phase. CAT2 expression was higher in both very young and senescent leaves, whereas CAT1 mRNA accumulated mainly in mature leaf, where the lowest CAT2 expression occurred. CAT1 and CAT2 are also differentially expressed in root, sprout and petal. Expression and activity patterns are consistent with different physiological roles for CAT1 and CAT2 isoforms. CAT1 is considered to be associated with photorespiration whereas CAT2 would fulfill physiological roles unrelated to this process. CAT2 appears to be a multifunctional isoform, associated with glyoxysomal activity in leaf senescence, other processes in non-photosynthetic organs and defence, functions that in other solanaceous species are fulfilled by two different isoforms.

scholarly journals Patterns of Genomic Sequence Diversity among Their Simian Immunodeficiency Viruses Suggest that L'Hoest Monkeys (Cercopithecus lhoesti) Are a Natural Lentivirus Reservoir

2000 ◽  
Vol 74 (8) ◽  
pp. 3892-3898 ◽  
Author(s):  
Brigitte E. Beer ◽  
Elizabeth Bailes ◽  
George Dapolito ◽  
Barbara J. Campbell ◽  
Robert M. Goeken ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Democratic Republic ◽  
Genomic Sequence ◽  
Democratic Republic Of Congo ◽  
Vervet Monkeys ◽  
Genome Sequences ◽  
Distinct Cluster ◽  
Immunodeficiency Virus ◽  
Genomic Regions ◽  
Full Length Genome

ABSTRACT Recently, we described a novel simian immunodeficiency virus (SIVlhoest) from a wild-caught L'Hoest monkey (Cercopithecus lhoesti) from a North American zoo. To investigate whether L'Hoest monkeys are the natural host for these viruses, we have screened blood samples from 14 wild animals from the Democratic Republic of Congo. Eight (57%) were found to be seropositive for SIV. Nearly full-length genome sequences were obtained for SIV isolates from three of these monkeys and compared to the original isolate and to other SIVs. The four samples of SIVlhoest formed a distinct cluster in phylogenetic trees. Two of these isolates differed on average at only about 5% of nucleotides, suggesting that they were epidemiologically linked; otherwise, the SIVlhoest isolates differed on average by 18%. Both the level of diversity and the pattern of its variation along the genome were very similar to those seen among isolates of SIVagm from vervet monkeys, pointing to similarities in the nature of, and constraints on, SIV evolution in these two species. Discordant phylogenetic relationships among the SIVlhoest isolates for different genomic regions indicated that mosaic viruses have been generated by recombination, implying that individual monkeys have been coinfected by more than one strain of SIV. Taken together, these observations provide strong evidence that L'Hoest monkeys constitute a natural reservoir for SIV.

scholarly journals Diversity of the genus Lactobacillus revealed by comparative genomics of five species

Microbiology ◽  
2006 ◽  
Vol 152 (11) ◽  
pp. 3185-3196 ◽  
Author(s):  
Carlos Canchaya ◽  
Marcus J. Claesson ◽  
Gerald F. Fitzgerald ◽  
Douwe van Sinderen ◽  
Paul W. O'Toole
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Whole Genome ◽  
Genome Sequences ◽  
Lactobacillus Salivarius ◽  
Core Proteins ◽  
Genus Lactobacillus ◽  
High Level

The genus Lactobacillus contains over 80 recognized species, and is characterized by a high level of diversity, reflected in its complex phylogeny. The authors' recent determination of the genome sequence of Lactobacillus salivarius means that five complete genomes of Lactobacillus species are available for comparative genomics: L. salivarius, L. plantarum, L. acidophilus, L. johnsonii and L. sakei. This paper now shows that there is no extensive synteny of the genome sequences of these five lactobacilli. Phylogeny based on whole-genome alignments suggested that L. salivarius was closer to L. plantarum than to L. sakei, which was closest to Enterococcus faecalis, in contrast to 16S rRNA gene relatedness. A total of 593 orthologues common to all five species were identified. Species relatedness based on this protein set was largely concordant with genome synteny-based relatedness. A Lactobacillus supertree, combining individual phylogenetic trees from each of 354 core proteins, had four main branches, comprising L. salivarius–L. plantarum; L. sakei; E. faecalis; and L. acidophilus–L. johnsonii. The extreme divergence of the Lactobacillus genomes analysed supports the recognition of new subgeneric divisions.

scholarly journals Reassortment Network of Influenza A Virus

2021 ◽  
Vol 12 ◽  
Author(s):  
Xingfei Gong ◽  
Mingda Hu ◽  
Wei Chen ◽  
Haoyi Yang ◽  
Boqian Wang ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Minimum Spanning Tree ◽  
Comprehensive Understanding ◽  
Genome Sequences ◽  
Genetic Characteristics ◽  
Time Period ◽  
Genome Wide ◽  
History Of

Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments. Genetic exchange through reassortment of the segmented genomes often endows IAVs with new genetic characteristics, which may affect transmissibility and pathogenicity of the viruses. However, a comprehensive understanding of the reassortment history of IAVs remains lacking. To this end, we assembled 40,296 whole-genome sequences of IAVs for analysis. Using a new clustering method based on Mean Pairwise Distances in the phylogenetic trees, we classified each segment of IAVs into clades. Correspondingly, reassortment events among IAVs were detected by checking the segment clade compositions of related genomes under specific environment factors and time period. We systematically identified 1,927 possible reassortment events of IAVs and constructed their reassortment network. Interestingly, minimum spanning tree of the reassortment network reproved that swine act as an intermediate host in the reassortment history of IAVs between avian species and humans. Moreover, reassortment patterns among related subtypes constructed in this study are consistent with previous studies. Taken together, our genome-wide reassortment analysis of all the IAVs offers an overview of the leaping evolution of the virus and a comprehensive network representing the relationships of IAVs.

scholarly journals Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events

2021 ◽  
Author(s):  
Edward Susko ◽  
Mike Steel ◽  
Andrew J. Roger
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Edge Length ◽  
Eukaryotic Cells ◽  
High Profile ◽  
Large Sets ◽  
Different Origins ◽  
Alternative Set ◽  
Strict Molecular Clock

AbstractTwo recent high profile studies have attempted to use edge (branch) length ratios from large sets of phylogenetic trees to determine the relative ages of genes of different origins in the evolution of eukaryotic cells. This approach can be straightforwardly justified if substitution rates are constant over the tree for a given protein. However, such strict molecular clock assumptions are not expected to hold on the billion-year timescale. Here we propose an alternative set of conditions under which comparisons of edge length distributions from multiple sets of phylogenies of proteins with different origins can be validly used to discern the order of their origins. We also point out scenarios where these conditions are not expected to hold and caution is warranted.

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