scholarly journals Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

2022 ◽  
Author(s):  
Raz Avni ◽  
Thomas Lux ◽  
Anna Minz‐Dub ◽  
Eitan Millet ◽  
Hanan Sela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Aegilops Species ◽  
Genome Sequences ◽  
Wheat Improvement

scholarly journals Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity

2017 ◽  
Vol 5 (50) ◽  
Author(s):  
Jayanthi Gangiredla ◽  
Mark K. Mammel ◽  
Tammy J. Barnaba ◽  
Carmen Tartera ◽  
Solomon T. Gebru ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Human Health ◽  
Potential Risk ◽  
Phylogenetic Relationships ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli

ABSTRACT Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We report the genome sequences of 2,244 E. coli isolates from multiple animal and environmental sources. Their phylogenetic relationships and potential risk to human health were examined.

scholarly journals Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic

2020 ◽  
Author(s):  
Tetsuro Kawano-Sugaya ◽  
Koji Yatsu ◽  
Tsuyoshi Sekizuka ◽  
Kentaro Itokawa ◽  
Masanori Hashino ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Phylogenetic Relationships ◽  
Viral Genome ◽  
Functional Limitations ◽  
Time Dependent ◽  
Network Visualization ◽  
Visualization Tool ◽  
Genome Sequences ◽  
Haplotype Networks ◽  
Cluster Visualization

AbstractThe worldwide eruption of COVID-19 that began in Wuhan, China in late 2019 reached 10 million cases by late June 2020. In order to understand the epidemiological landscape of the COVID-19 pandemic, many studies have attempted to elucidate phylogenetic relationships between collected viral genome sequences using haplotype networks. However, currently available applications for network visualization are not suited to understand the COVID-19 epidemic spatiotemporally, due to functional limitations That motivated us to develop Haplotype Explorer, an intuitive tool for visualizing and exploring haplotype networks. Haplotype Explorer enables people to dissect epidemiological consequences via interactive node filters to provide spatiotemporal perspectives on multimodal spectra of infectious diseases, including introduction, outbreak, expansion, and containment, for given regions and time spans. Here, we demonstrate the effectiveness of Haplotype Explorer by showing an example of its visualization and features. The demo using SARS-CoV-2 genome sequences is available at https://github.com/TKSjp/HaplotypeExplorerSummaryA lot of software for network visualization are available, but existing software have not been optimized to infection cluster visualization against the current worldwide invasion of COVID-19 started since 2019. To reach the spatiotemporal understanding of its epidemics, we developed Haplotype Explorer. It is superior to other applications in the point of generating HTML distribution files with metadata searches which interactively reflects GISAID IDs, locations, and collection dates. Here, we introduce the features and products of Haplotype Explorer, demonstrating the time-dependent snapshots of haplotype networks inferred from total of 4,282 SARS-CoV-2 genomes.

Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae)

Genome ◽  
2012 ◽  
Vol 55 (3) ◽  
pp. 177-193 ◽  
Author(s):  
B.R. Baum ◽  
T. Edwards ◽  
M. Mamuti ◽  
D.A. Johnson
Keyword(s):  
Phylogenetic Relationships ◽  
5S Rdna ◽  
Reticulate Evolution ◽  
Evolutionary Relationships ◽  
Aegilops Species ◽  
Polyploid Species ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Cytogenetic Analyses

Phylogenetic inferences of the polyploid Aegilops taxa were drawn based upon the analysis of 909 nuclear 5S rDNA sequences obtained from 15 Aegilops polyploid taxa (531 sequences new to this paper) and 378 sequences from our previous study on the diploid taxa. The 531 sequences can be split into two orthologous groups (unit classes), the long AE1 and short AE1 previously identified in the diploid set. An examination of the relationships between unit classes and their associated haplomes suggests that U haplome sequences found in Ae. umbellulata are the closest to the T sequences found in Amblyopyrum muticum and that sequences of the polyploid species expected to be the M type found in Ae. comos are more similar to the T haplome sequences, except in the three hexaploids Ae. glumiaristata, Ae. juvenalis, and Ae. vavilovii and the tetraploid Ae. crassa where they are found to be similar to the M haplome sequences. These three hexaploid taxa likely originated from the tetraploid Ae. crassa (DM), while the closest taxon to the fourth hexaploid, Ae. recta, is the tetraploid Ae. neglecta (UM). Based upon the distribution of the unit classes, several reticulate phylogenies depicting evolutionary relationships among diploid, tetraploid, and hexaploid taxa were constructed; however, none of these widely used methods could depict the expected reticulate relationship as previously drawn from cytogenetic analyses in this group of allopolyploid species. These results suggest that evolutionary relationships derived from models based upon the assumption of bifurcating species require careful interpretation when these same models are applied to species with reticulate evolution.

scholarly journals Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

2021 ◽  
Author(s):  
Raz Avni ◽  
Thomas Lux ◽  
Anna Minz-Dub ◽  
Eitan Millet ◽  
Hanan Sela ◽  
...  
Keyword(s):  
Haplotype Block ◽  
Close Relative ◽  
Whole Genome ◽  
Aegilops Species ◽  
Wheat Improvement ◽  
Genome Wide ◽  
Triticum Spp ◽  
Species Specific ◽  
Genomic Regions ◽  
Genome Assemblies

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly simiar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

scholarly journals Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

2018 ◽  
Vol 123 (5) ◽  
pp. 857-865 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Ovidiu Paun ◽  
Mark W Chase ◽  
Peter S Ashton ◽  
A S Kamariah ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Plastid Genomes ◽  
Snp Data ◽  
Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

scholarly journals Draft Genome Sequences of Escherichia coli Strains Isolated at Calving from the Uterus, Vagina, Vulva, and Rectoanal Junction of a Dairy Cow That Later Developed Metritis

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Soo Jin Jeon ◽  
Federico Cunha ◽  
Amber Ginn ◽  
KwangCheol Casey Jeong ◽  
Klibs N. Galvão
Keyword(s):  
Escherichia Coli ◽  
Dairy Cow ◽  
Phylogenetic Relationships ◽  
Draft Genome ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Insight Into

ABSTRACT Escherichia coli is involved in the pathogenicity of metritis in cows. We report here the genome sequences of E. coli strains isolated at calving from the uterus, vagina, vulva, and rectoanal junction of a dairy cow that later developed metritis. The genomic similarities will give an insight into phylogenetic relationships among strains.

scholarly journals The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6320 ◽  
Author(s):  
Zhen Yang ◽  
Guixi Wang ◽  
Qinghua Ma ◽  
Wenxu Ma ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Molecular Dating ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Genome Variation ◽  
Genome Data ◽  
Chloroplast Genomes

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

scholarly journals Genomic architecture and introgression shape a butterfly radiation

Science ◽  
2019 ◽  
Vol 366 (6465) ◽  
pp. 594-599 ◽  
Author(s):  
Nathaniel B. Edelman ◽  
Paul B. Frandsen ◽  
Michael Miyagi ◽  
Bernardo Clavijo ◽  
John Davey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Color Pattern ◽  
Lineage Sorting ◽  
Genome Sequences ◽  
Genomic Architecture ◽  
Genome Assemblies

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.

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