scholarly journals Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tingting Li ◽  
Dongxia Liu ◽  
Yadi Yang ◽  
Jiali Guo ◽  
Yujie Feng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Virus Disease ◽  
Evolutionary Relationship ◽  
Critical Issue ◽  
Last Common Ancestor ◽  
Phylogenetic Tree Analysis ◽  
Origin And Evolution ◽  
Supertree Method ◽  
The Matrix

AbstractCorona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

scholarly journals Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

2020 ◽  
Author(s):  
Tingting Li ◽  
Dongxia Liu ◽  
Yadi Yang ◽  
Jiali Guo ◽  
Yujie Feng ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Common Ancestor ◽  
Virus Disease ◽  
Evolutionary Relationship ◽  
Critical Issue ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Phylogenetic Tree Analysis ◽  
Origin And Evolution ◽  
Bat Coronavirus

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

scholarly journals A Comparative Genomic and Phylogenetic Analysis of the Origin and Evolution of the CCN Gene Family

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Kuan Hu ◽  
Yiming Tao ◽  
Juanni Li ◽  
Zhuang Liu ◽  
Xinyan Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Evolutionary Relationship ◽  
Evolutionary Process ◽  
Structural Features ◽  
Comparative Genomic ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Origin And Evolution ◽  
Functional Sites

CCN gene family members have recently been identified as multifunctional regulators involved in diverse biological functions, especially in vascular and skeletal development. In the present study, a comparative genomic and phylogenetic analysis was performed to show the similarities and differences in structure and function of CCNs from different organisms and to reveal their potential evolutionary relationship. First, CCN homologs of metazoans from different species were identified. Then we made multiple sequence alignments, MEME analysis, and functional sites prediction, which show the highly conserved structural features among CCN metazoans. The phylogenetic tree was further established, and thus CCNs were found undergoing extensive lineage-specific duplication events and lineage-specific expansion during the evolutionary process. Besides, comparative analysis about the genomic organization and chromosomal CCN gene surrounding indicated a clear orthologous relationship among these species counterparts. At last, based on these research results above, a potential evolutionary scenario was generated to overview the origin and evolution of the CCN gene family.

scholarly journals ANALISIS FILOGENETIK GARCINIA SPP. BERDASARKAN SEKUENS GEN rRNA

2021 ◽  
Vol 46 (2) ◽  
pp. 259
Author(s):  
Rara Erlina Oktafia ◽  
Badruzsaufari Badruzsaufari
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Gene Sequence ◽  
Maximum Likelihood Method ◽  
Evolutionary Relationship ◽  
Morphological Characters ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Garcinia genus has a complicated taxonomy due to the high similarities in morphological characters of its members. The phylogenetic analysis on Garcinia species based on rRNA gene sequence intended to find out the evolutionary relationship amongst the species. This research employed 20 sequences of the rRNA gene of Garcinia species selected from the GenBank of the National Center for Biology Information (NCBI).  The sequences were aligned using ClustalW with the MEGA X application. A phylogenetic tree was constructed Maximum Likelihood method approximation and Kimura 2-parameter model. The results of the analysis showed that the cladogram had monophyletic parameter properties and classified into 3 clades. Clade I consisted of G. celebica, G. hombroniana, G. opaca, G. mangostana, G. malaccensis, G. penangiana, G. scortechinii, G. hanburyi, and G. urophylla. Clade II included G. atroviridis, G. bancana, G. forbesii, G. griffithii, G. cowa, G. nigrolineata, G. globulosa, and G. parvifolia. Clade III composed of G. rostrata, G. nervosa, and G. praininiana.  The species of Garcinia considered the most primitive and the closet to their ancestor is G. nervosa. 

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

Rhizocarpon smaragdulum, a new monosporic yellow-thalline species and some additional species of the genus Rhizocarpon from the Altai Mountains (Siberia)

2017 ◽  
Vol 49 (5) ◽  
pp. 457-466 ◽  
Author(s):  
Evgeny A. DAVYDOV ◽  
Lidia S. YAKOVCHENKO
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Altai Mountains ◽  
Additional Species ◽  
Sister Relationship

AbstractRhizocarpon smaragdulum Davydov & Yakovchenko sp. nov. is described and a phylogenetic analysis (ITS, mtSSU) is presented, confirming its distinctiveness and indicating a sister relationship with R. suomiense and R. subgeminatum. The species is unique among yellow Rhizocarpon species in having a single hyaline ascospore per ascus. The phylogenetic tree suggests that the number of ascospores per ascus has been reduced in Rhizocarpon more than once during the course of its evolution. Two new distributional records are also reported: Rhizocarpon atroflavescens is new for Siberia and R. norvegicum is new for the Altai Mountains. Rhizocarpon norvegicum in this region grows on rocks and is also lichenicolous on Acarospora bullata.

A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

2021 ◽  
Vol 9 (1) ◽  
pp. 49-55
Author(s):  
Vanlal hruaia ◽  
◽  
Lal rinmuana ◽  
J Lalbiaknunga ◽  
Laldinfeli Ralte
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Flowering Plants ◽  
Morphological Features ◽  
Total Evidence ◽  
Pictorial Representation ◽  
Phenetic Analysis ◽  
Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain

Nematology ◽  
2011 ◽  
Vol 13 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Blanca Landa ◽  
Carolina Cantalapiedra-Navarrete ◽  
Juan Palomares-Rius ◽  
Pablo Castillo ◽  
Carlos Gutiérrez-Gutiérrez
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Matrix Representation ◽  
Natural Environments ◽  
28S Rrna ◽  
Parsimony Method ◽  
Rdna Genes ◽  
Supertree Method ◽  
The Matrix ◽  
Relationship Of

AbstractDuring a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz., the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum, X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank.

Molecular Analysis of Hepatitis B Virus in Mothers-Children Pairs

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chatzidaki V ◽  
◽  
Perdikogianni C ◽  
Galanakis E ◽  
Paraskevis D ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Phylogenetic Tree ◽  
Surface Glycoprotein ◽  
Phylogenetic Tree Analysis ◽  
Source Of Infection ◽  
B Virus ◽  
Maximum Likelihood Methods ◽  
Infection Source ◽  
Relationship Of

ackground: Vertical transmission of Hepatitis B Virus (HBV) is the primary infection source for infants, but little is known on the proportion of children that have acquired HBV from their mothers. Objective: We investigated the relationship of HBV sequencing in HBVpositive children and their mothers and explored the HBV phylogenetic tree. Methods: Serum-extracted HBV-DNA from 38 individuals (13 children paired to nine mothers, 16 unpaired infected children) was amplified by polymerase chain reaction and the target region HBV surface glycoprotein (amino acids 40-171) was directly sequenced. Following editing and alignment of these sequences, phylogenetic tree analysis was performed using the neighbourjoining and maximum-likelihood methods. Results: Analysis was successfully performed in 29 subjects (23 children and six mothers), including six mother-child pairs. All individuals were infected by genotype D. Subgenotype adw3 prevailed (21, 72.4%), followed by ayw2 (4, 13.8%) and ayw3 (4, 13.8%). Among six mother-child pairs, three had identical and three had different subgenotypes. Phylogenetic analysis revealed that HBV sequences from three children did not cluster with their siblings suggesting a different source of infection. Conclusion: Our findings suggest that HBV subgenotypes in infected children may not be identical to their mothers’ and point to non-vertical HBV transmission in childhood.

Morphological evidence for paraphyly of Holopothrips Hood (Thysanoptera: Phlaeothripidae), a Neotropical genus of gall-inducing thrips

2021 ◽  
pp. 1-24
Author(s):  
Mariana F. Lindner ◽  
Augusto Ferrari ◽  
Adriano Cavalleri
Keyword(s):  
Phylogenetic Analysis ◽  
Host Plants ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Morphological Evidence ◽  
Diverse Group ◽  
The Matrix ◽  
Internal Relations ◽  
Evolutionary Story

Abstract Holopothrips is a diverse group of thrips associated to galls in the Neotropics, with a variety of host plants and wide morphological diversity. Relationships to other Neotropical groups have been proposed, but are still untested, and the monophyly of the genus remains doubtful. Here, we perform a phylogenetic analysis of Holopothrips, based on morphological characters. A total of 87 species were included in the matrix and eight analyses were carried out, but all of them failed to recover Holopothrips as a monophyletic grouping. Bremer and Bootstrap support values were low, and the topologies varied among all analyses, with uncertain internal relations for the ingroup. These results indicate that the relationships for Holopothrips species, and the proposed related genera, are more complex than previously reported; and morphological characters may not be enough to recover the evolutionary story within this group. We also discuss the influences of different character coding, continuous characters and weighting schemes in our results.

Sign in / Sign up

Export Citation Format

Share Document