scholarly journals Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Welkin H Pope ◽  
Charles A Bowman ◽  
Daniel A Russell ◽  
Deborah Jacobs-Sera ◽  
David J Asai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Smegmatis ◽  
Scientific Discovery ◽  
Genome Comparison ◽  
Sequence Comparisons ◽  
Rarefaction Analysis ◽  
Large Numbers ◽  
Single Host ◽  
Structured Program ◽  
Phage Isolation

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

scholarly journals Large numbers of vertebrates began rapid population decline in the late 19th century

2016 ◽  
Vol 113 (49) ◽  
pp. 14079-14084 ◽  
Author(s):  
Haipeng Li ◽  
Jinggong Xiang-Yu ◽  
Guangyi Dai ◽  
Zhili Gu ◽  
Chen Ming ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Threatened Species ◽  
Driving Forces ◽  
Population Decline ◽  
Cumulative Effect ◽  
Extinction Time ◽  
Time Period ◽  
Large Numbers ◽  
The Difference

Accelerated losses of biodiversity are a hallmark of the current era. Large declines of population size have been widely observed and currently 22,176 species are threatened by extinction. The time at which a threatened species began rapid population decline (RPD) and the rate of RPD provide important clues about the driving forces of population decline and anticipated extinction time. However, these parameters remain unknown for the vast majority of threatened species. Here we analyzed the genetic diversity data of nuclear and mitochondrial loci of 2,764 vertebrate species and found that the mean genetic diversity is lower in threatened species than in related nonthreatened species. Our coalescence-based modeling suggests that in many threatened species the RPD began ∼123 y ago (a 95% confidence interval of 20–260 y). This estimated date coincides with widespread industrialization and a profound change in global living ecosystems over the past two centuries. On average the population size declined by ∼25% every 10 y in a threatened species, and the population size was reduced to ∼5% of its ancestral size. Moreover, the ancestral size of threatened species was, on average, ∼22% smaller than that of nonthreatened species. Because the time period of RPD is short, the cumulative effect of RPD on genetic diversity is still not strong, so that the smaller ancestral size of threatened species may be the major cause of their reduced genetic diversity; RPD explains 24.1–37.5% of the difference in genetic diversity between threatened and nonthreatened species.

scholarly journals Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam

2014 ◽  
Vol 95 (3) ◽  
pp. 549-556 ◽  
Author(s):  
Nguyen Van Dung ◽  
Pham Hong Anh ◽  
Nguyen Van Cuong ◽  
Ngo Thi Hoa ◽  
Juan Carrique-Mas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Untranslated Region ◽  
Study Group ◽  
Group Comparison ◽  
Specific Primers ◽  
Sequence Comparisons ◽  
Detection Rates ◽  
High Frequencies ◽  
Faecal Samples

Picornaviruses infecting pigs, described for many years as ‘porcine enteroviruses’, have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5′ untranslated region (5′ UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90 % in recently weaned pigs but declining to 40 % in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74 % (n = 70) compared with 72 % (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified EV-G types. These have now been formally assigned as EV-G types 8–11 by the Picornavirus Study Group. Comparison of VP1, VP4/VP2, 3Dpol and 5′ UTRs of study samples and those available on public databases showed frequent, bootstrap-supported differences in their phylogenies indicative of extensive within-species recombination between genome regions. In summary, we identified extremely high frequencies of infection with EV-G in pigs in Vietnam, substantial genetic diversity and recombination within the species, and evidence for a much larger number of circulating EV-G types than currently described.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

scholarly journals Cyanobiont-bearing Dinoflagellate Ornithocercus in Temperate Coastal Waters: Cyanobiont Genetic Diversity and Host Specificity

2020 ◽  
Author(s):  
Miran Kim ◽  
Dong Choi ◽  
Myung Park
Keyword(s):  
Genetic Diversity ◽  
Coastal Waters ◽  
Host Cells ◽  
Genetic Types ◽  
Four Seasons ◽  
Wide Range ◽  
Single Host ◽  
Unicellular Organisms ◽  
Miseq Platform ◽  
Bacterial Groups

Abstract Cyanobacteria are ubiquitous in marine environments and play an important role as primary producers. Some cyanobacteria, the so called cyanobionts (cyanobacterial symbionts), have a symbiotic relationship with unicellular organisms. Among these relationships, in particular, the nature (e.g., genetic diversity, host or cyanobiont specificity, and cyanobionts seasonality) of the cyanobionts-dinoflagellate host consortia remain poorly understood. In this study, 16S rDNA of cyanobionts in a total of 138 single host cells isolated over four seasons in temperate waters were sequenced using the MiSeq platform. Genetic analysis of cyanobionts from the dinoflagellate host Ornithocercus revealed that three genetic types of Synechococcales cyanobionts occurred at a wide range of water temperatures (11–24°C) and their distribution seems to be closely associated with the variation in salinity. Furthermore, this study showed the presence of some degree of host (or cyanobiont) specificity in cyanobionts (or host) among Ornithocercus species as well as among other dinophysoid species (i.e. Amphisolenia, Citharistes, and Histioneis). In addition to Synechococcales cyanobionts, this study identified some OTU sequences affiliated with the Vampirovibrionales and Chroococcidiopsidales in some Ornithocercus cells, suggesting that Ornithocercus species seem to be an additional new habitat for those bacterial groups.

scholarly journals Genetic Diversity Among Geminiviruses Associated with the Weed Species Sida spp., Macroptilium lathyroides, and Wissadula amplissima from Jamaica

Plant Disease ◽  
1997 ◽  
Vol 81 (11) ◽  
pp. 1251-1258 ◽  
Author(s):  
Marcia E. Roye ◽  
Wayne A. McLaughlin ◽  
Medhat K. Nakhla ◽  
Douglas P. Maxwell
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Mosaic Virus ◽  
Amino Acid Sequences ◽  
Yellow Mosaic Virus ◽  
Weed Species ◽  
Degenerate Primers ◽  
Sequence Comparisons ◽  
The Common ◽  
Macroptilium Lathyroides

Genetic diversity among geminiviruses associated with three common weeds in Jamaica was studied using digoxigenin-labeled geminiviral DNA probes, polymerase chain reaction with degenerate primers for DNA-A and DNA-B, nucleic acid sequencing, and derived amino acid sequences. Geminiviruses with bipartite genomes were found in Sida spp., Macroptilium lathyroides, and Wissadula amplissima. The geminiviruses detected in Sida spp. and M. lathyroides were nearly identical and were both designated Sida golden mosaic geminivirus (SidGMV-JA), whereas the geminivirus in W. amplissima was sufficiently different to be designated Wissadula golden mosaic geminivirus (WGMV). Nucleotide sequence comparisons of the common regions and the N-terminal regions of the AC1 (rep) and AV1 ORFs, together with the derived amino acid sequence comparisons of the N-terminal parts of BC1 and BV1 ORFs were used to determine their similarities to other geminiviruses. SidGMV-JA was most similar to potato yellow mosaic geminivirus (PYMV). We propose that these two geminiviruses (SidGMV-JA and PYMV) define a new geminivirus cluster, the potato yellow mosaic virus (PYMV) cluster. WGMV was most similar to members of the Abutilon mosaic virus cluster but is not likely to be included in the Abutilon phylogenetic group because of the divergent sequence of the common region. These results indicate that geminiviruses infecting some weeds in Jamaica are distinct from crop-infecting geminiviruses in Jamaica and define a new geminivirus cluster.

scholarly journals Diet breadth and its relationship with genetic diversity and differentiation: the case of southern beech aphids (Hemiptera: Aphididae)

2004 ◽  
Vol 94 (3) ◽  
pp. 219-227 ◽  
Author(s):  
C. Gaete-Eastman ◽  
C.C. Figueroa ◽  
R. Olivares-Donoso ◽  
H.M. Niemeyer ◽  
C.C. Ramírez
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Diet Breadth ◽  
Aphid Species ◽  
Insect Species ◽  
Herbivorous Insect ◽  
Genetic Structuring ◽  
Closely Related Species ◽  
Single Host ◽  
Southern Beech

AbstractHerbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation than insect species with a wider diet breadth. However, a generalist can behave as a local specialist if a single host-plant species is locally available, while a specialist can eventually behave as a generalist if its preferred host is not available. These problems can be addressed by comparing closely related species differing in diet breadth with overlapping distributions of insect and host populations. In this work, diet breadth, genetic diversity and population differentiation of congeneric aphid species from southern beech forests in Chile were compared. While at the species level no major differences in genetic diversity were found, a general trend towards higher genetic diversity as diet breadth increased was apparent. The aphid species with wider diet breadth, Neuquenaphis edwardsi (Laing), showed the highest genetic diversity, while the specialist Neuquenaphis staryi Quednau & Remaudière showed the lowest. These differences were less distinct when the comparisons were made in the same locality and over the same host. Comparison of allopatric populations indicates that genetic differentiation was higher for the specialists, Neuquenaphis similis Hille Ris Lambers and N. staryi, than for the generalist N. edwardsi. Over the same host at different locations, genetic differentiation among populations of N. edwardsi was higher than among populations of N. similis. The results support the assumption that specialists should show more pronounced genetic structuring than generalists, although the geographical distribution of host plants may be playing an important role.

scholarly journals Comparison of Genetic Diversity in Core and Whole Germplasm Collections for Phaseolus vulgaris L.

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 772E-772
Author(s):  
J. Nienhuis ◽  
P. Skroch ◽  
M. Sass ◽  
S. Beebe ◽  
J. Tohme ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Phaseolus Vulgaris L ◽  
The Core ◽  
Germplasm Collections ◽  
Large Numbers ◽  
Random Samples ◽  
Two Samples ◽  
Marker Frequency ◽  
Seed Characteristics

The number of Phaseolus vulgaris germplasm accessions numbers more than 30,000. While the large numbers of accessions increase the probability of preserving genetic variability they simultaneously limit the efficient and routine utilization of this resource. From the approximately 4000 P. vulgaris accessions in the C.I.A.T. whole collection that were collected in Mexico, a core collection of 400 accessions was developed based on variation for agronomic performance, ecological adaptation, and seed characteristics. Random samples of 90 accessions each were drawn from the core and whole collections and evaluated for 224 polymorphic RAPD bands. Based on analysis of the RAPD data there were no significant differences in genetic diversity between the two samples. The correlation of marker frequency for the two samples was 0.984 confirming that the two samples represent the same population.

scholarly journals Combining Strengths for Multi-genome Visual Analytics Comparison

2019 ◽  
Vol 13 ◽  
pp. 117793221882512 ◽  
Author(s):  
Sergio Diaz-del-Pino ◽  
Pablo Rodriguez-Brazzarola ◽  
Esteban Perez-Wohlfeil ◽  
Oswaldo Trelles
Keyword(s):  
Data Analysis ◽  
Data Acquisition ◽  
Visual Analytics ◽  
Large Scale ◽  
Visual Analysis ◽  
Homo Sapiens ◽  
Third Party ◽  
Genome Comparison ◽  
Post Processing ◽  
Sequence Comparisons

The eclosion of data acquisition technologies has shifted the bottleneck in molecular biology research from data acquisition to data analysis. Such is the case in Comparative Genomics, where sequence analysis has transitioned from genes to genomes of several orders of magnitude larger. This fact has revealed the need to adapt software to work with huge experiments efficiently and to incorporate new data-analysis strategies to manage results from such studies. In previous works, we presented GECKO, a software to compare large sequences; now we address the representation, browsing, data exploration, and post-processing of the massive amount of information derived from such comparisons. GECKO-MGV is a web-based application organized as client-server architecture. It is aimed at visual analysis of the results from both pairwise and multiple sequences comparison studies combining a set of common commands for image exploration with improved state-of-the-art solutions. In addition, GECKO-MGV integrates different visualization analysis tools while exploiting the concept of layers to display multiple genome comparison datasets. Moreover, the software is endowed with capabilities for contacting external-proprietary and third-party services for further data post-processing and also presents a method to display a timeline of large-scale evolutionary events. As proof-of-concept, we present 2 exercises using bacterial and mammalian genomes which depict the capabilities of GECKO-MGV to perform in-depth, customizable analyses on the fly using web technologies. The first exercise is mainly descriptive and is carried out over bacterial genomes, whereas the second one aims to show the ability to deal with large sequence comparisons. In this case, we display results from the comparison of the first Homo sapiens chromosome against the first 5 chromosomes of Mus musculus.

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