scholarly journals Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1476
Author(s):  
Lester J. Perez ◽  
Gavin A. Cloherty ◽  
Michael G. Berg
Keyword(s):  
Genetic Diversity ◽  
Sequence Comparison ◽  
Complete Resolution ◽  
Pairwise Distance ◽  
Pairwise Sequence Comparison ◽  
Double Stranded Rna ◽  
Phylogenetic Marker ◽  
High Degree ◽  
Phylogenetic Noise

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

scholarly journals PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

Viruses ◽  
2012 ◽  
Vol 4 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Yiming Bao ◽  
Vyacheslav Chetvernin ◽  
Tatiana Tatusova
Keyword(s):  
Sequence Comparison ◽  
Pairwise Sequence Comparison

scholarly journals Assessment of genetic diversity in Indian Barnyard millet (Echinochloa spp. complex) using morphological and molecular markers

2016 ◽  
Vol 8 (3) ◽  
pp. 1643-1648 ◽  
Author(s):  
M. P. Moharil ◽  
Dipti Gawai ◽  
N. Dikshit ◽  
M.S. Dudhare ◽  
P. V. Jadhav
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Improvement ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Barnyard Millet ◽  
Clear Cut ◽  
Cultivated Species ◽  
High Degree

In the present study, morphological and molecular markers (RAPD primers) were used to analyze the genetic diversity and genetic relationships among 21 accessions of Echinochloa spp. complex comprising the wild and cultivated species collected from Melghat and adjoining regions of Vidarbha, Maharashtra. The availability of diverse genetic resources is a prerequisite for genetic improvement of any crop including barnyard millet. A high degree of molecular diversity among the landraces was detected. Among the 21 genotypes, two major groups (A and B) were formed, at 67.28 % similarity, which clearly encompasses 15 accessions of E. frumentacea and 6 accessions of E. colona. Higher similarity was observed in accessions of E. frumentacea. The accessions IC 597322 and IC 597323 also IC 597302 and IC 597304 showed more than 94% similarity among themselves. The classification of genetic diversity has enabled clear-cut grouping of barnyard millet accessions into two morphological races (E. frumentacea and E. colona).

Genomic Relations among Two Non-mangrove and Nine Mangrove Species of Indian Rhizophoraceae

2004 ◽  
Vol 59 (7-8) ◽  
pp. 572-578 ◽  
Author(s):  
Arup Kumar Mukherjee ◽  
Laxmikanta Acharya ◽  
Pratap Chandra Panda ◽  
Trilochan Mohapatra ◽  
Premananda Das
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Genomic Relationship ◽  
Mangrove Species ◽  
The Family ◽  
And Cluster Analysis ◽  
High Degree

AbstractRandom amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to study the genomic relationship among 11 members of Indian Rhizophoraceae represented by nine true mangroves and two non-mangrove species. The AFLP and RAPD bands were scored and analyzed for genetic similarities and cluster analysis was done which separated the 11 species studied into two main groups, the true mangroves and the non-mangroves. The polymorphism observed for these markers showed a high degree of genetic diversity among the constituent taxa of the family. The phylogenetic relationship inferred from molecular marker systems supported the traditional taxonomic classification of the family Rhizophoraceae based on morphological characters at the levels of tribe, phylogeny and delimitation of genera and species, except the intra-generic classification of the genus Bruguiera and the placement of Rhizophora in the family Rhizophoraceae.

scholarly journals Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan

2014 ◽  
Vol 95 (9) ◽  
pp. 1945-1957 ◽  
Author(s):  
Asif Naeem ◽  
Takushi Hosomi ◽  
Yorihiro Nishimura ◽  
Muhammad Masroor Alam ◽  
Tomoichiro Oka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Diversity ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Full Genome Sequence ◽  
Emerging Viruses ◽  
High Genetic Diversity ◽  
Genotype Assignment ◽  
Pcr Targeting

Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5′ untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler’s murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41–56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

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