scholarly journals Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus

2018 ◽  
Author(s):  
Casey M. Bergman
Keyword(s):  
Horizontal Transfer ◽  
Sensu Stricto ◽  
South American ◽  
Patchy Distribution ◽  
Reciprocal Translocations ◽  
Saccharomyces Paradoxus ◽  
Long Read ◽  
History Of ◽  
Genome Assemblies ◽  
Donor Species

AbstractBackgroundRecent evidence suggests that horizontal transfer plays a significant role in the evolution of of transposable elements (TEs) in eukaryotes. Many cases of horizontal TE transfer (HTT) been reported in animals and plants, however surprisingly few examples of HTT have been reported in fungi.FindingsHere I report evidence for a novel HTT event in fungi involving Tsu4 in Saccharomyces paradoxus based on (i) high similarity between Tsu4 elements in S. paradoxus and S. uvarum, (ii) a patchy distribution of Tsu4 in S. paradoxus and general absence from its sister species S. cerevisiae, and (iii) discordance between the phylogenetic history of Tsu4 sequences and species in the Saccharomyces sensu stricto group. Available data suggests the HTT event likely occurred somewhere in the Nearctic, Neotropic or Indo-Australian part of the S. paradoxus species range, and that a lineage related to S. uvarum or S. eubayanus was the donor species. The HTT event has led to massive proliferation of Tsu4 in the South American lineage of S. paradoxus, which exhibits partial reproductive isolation with other strains of this species because of multiple reciprocal translocations. Full-length Tsu4 elements are associated with both breakpoints of one of these reciprocal translocations.ConclusionsThis work shows that comprehensive analysis of TE sequences in essentially-complete genome assemblies derived from long-read sequencing provides new opportunities to detect HTT events in fungi and other organisms. This work also provides support for the hypothesis that HTT and subsequent TE proliferation can induce genome rearrangements that contribute to post-zygotic isolation in yeast.

scholarly journals Contrasting evolutionary genome dynamics between domesticated and wild yeasts

2017 ◽  
Vol 49 (6) ◽  
pp. 913-924 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Population Level ◽  
Structural Rearrangements ◽  
Reciprocal Translocations ◽  
Genome Dynamics ◽  
Long Read ◽  
Wild Yeasts ◽  
Definition Of ◽  
Genome Assemblies

Abstract Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

scholarly journals Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yoichiro Nakatani ◽  
Prashant Shingate ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
Aravind Prasad ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
De Novo ◽  
Genome Structure ◽  
Origin And Evolution ◽  
Long Read ◽  
History Of ◽  
And Function ◽  
Genome Assemblies ◽  
Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

scholarly journals Whole genome sequencing,de novoassembly and phenotypic profiling for the new budding yeast speciesSaccharomyces jurei

2018 ◽  
Author(s):  
Samina Naseeb ◽  
Haya Alsammar ◽  
Tim Burgis ◽  
Ian Donaldson ◽  
Norman Knyazev ◽  
...  
Keyword(s):  
Sensu Stricto ◽  
The Other ◽  
Model Systems ◽  
Chromosomal Translocations ◽  
Phenotypic Analysis ◽  
Ecological Analysis ◽  
Saccharomyces Sensu Stricto ◽  
Ty Elements ◽  
History Of ◽  
Genome Assemblies

AbstractSaccharomyces sensu strictocomplex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies ofSaccharomyces jurei,a newly discoveredSaccharomyces sensu strictospecies from high altitude oaks. Phylogenetic and phenotypic analysis revealed thatS. jureiis a sister-species toS. mikatae,thanS. cerevisiae,andS. paradoxus.The karyotype ofS. jureipresents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared toS. cerevisiaegenome. Interestingly, while the rearrangement I/XIII is unique toS. jurei,the other is in common withS. mikataestrain IFO1815, suggesting shared evolutionary history of this species after the split betweenS. cerevisiaeandS. mikatae.The number of Ty elements differed in the new species, with a higher number of Ty elements present inS. jureithan inS. cerevisiae.Phenotypically, theS. jureistrain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947Tunder most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the othersensu strictospecies. Both strains were found to be better adapted to lower temperatures compared toS. cerevisiae.

Discovering the biogeographic history using predefined areas and explicit geographical data in the South American Liolaemus elongatus group (Iguania: Liolaemidae)

2020 ◽  
pp. 53-68
Author(s):  
Marai Ruiz
Keyword(s):  
South America ◽  
Current Distribution ◽  
Sensu Stricto ◽  
South American ◽  
Phylogenetic Hypothesis ◽  
Ancestral Area ◽  
Geographical Data ◽  
Biogeographic History ◽  
History Of ◽  
Founder Events

The genus Liolaemus includes 268 species, classified in two subgenera, Eulaemus and Liolaemus sensu stricto. The latter is formed by 12 monophyletic groups; one of them being the Liolaemus elongatus group, distributed in South America. We studied the biogeographic history of the L. elongatus group. We obtained a phylogenetic hypothesis recovering five main clades: the L. punmahuida, L. elongatus sensu stricto, L. kriegi, L. petrophilus and L. capillitas clades. Based on that hypothesis we obtained a time calibrated tree. The ancestral ranges were estimated applying three methodologies: DEC, DEC+j (using predefined areas) and GEM (using explicit geographical data). Our results show that the ancestral area of the L. elongatus group was located in central Argentina, and its divergence began around 11.5 Mya. From here, a combination of events (founder events and/or vicariances) led the species to their current distribution. Despite their differences, DEC+j and GEM show congruent results.

scholarly journals Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Yury A Barbitoff ◽  
Andrew G Matveenko ◽  
Anton B Matiiv ◽  
Evgeniia M Maksiutenko ◽  
Svetlana E Moskalenko ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Structural Features ◽  
Multiple Observations ◽  
Yeast Strains ◽  
Trace Back ◽  
Oxford Nanopore ◽  
Long Read ◽  
History Of ◽  
Variant Analysis ◽  
Yeast Genomes

Abstract Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.

scholarly journals Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Jean-Marc Aury ◽  
Benjamin Istace
Keyword(s):  
Single Molecule ◽  
Direct Consequence ◽  
High Quality ◽  
Sequencing Errors ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

Violence and Hopelessness in the Colombian Novels La Virgen de Los Sicarios and Satanás

2020 ◽  
Vol 10 (2) ◽  
pp. 48-65
Author(s):  
Alan G. Hartman
Keyword(s):  
Literary History ◽  
Gabriel Garcia Marquez ◽  
South American ◽  
Jose Asuncion Silva ◽  
Virgen De Los Sicarios ◽  
History Of ◽  
Drug Lord ◽  
History Of Violence ◽  
Nineteenth And Twentieth Centuries ◽  
American Nation

Abstract Colombia is a South American nation that has captured the imagination of the world. It is a land of beautiful colonial cities and towns, famous for coffee production, rich emerald mines, and the literature of José Asunción Silva and Gabriel García Márquez. Colombia’s beauty and rich literary history, however, are often overshadowed by the memory of Pablo Escobar, a notorious drug lord, and numerous deadly guerilla groups. Their roles in the international drug trade made Colombia the top producer and exporter of cocaine, which resulted in terrorism and violence that left the country one of the world’s most dangerous.1 In this article, I will explore how violence in Colombia has perpetuated the theme of hopelessness in the nation’s literature beginning in the mid-twentieth century. I will show this in three parts. Firstly, I will trace the history of violence in Colombia through the nineteenth and twentieth centuries and show that a literary genre of violence was absent in the nation until 1946, when the period known as “la Violencia” commenced. Secondly, I will explore how hopelessness resulted from violence in Colombia beginning in the period of “la Violencia.” Thirdly, I will show how violence is depicted as an evil that traps the protagonists of the contemporary Colombian novels La Virgen de Los Sicarios and Satanás in a state of hopelessness due to their powerlessness to truly change themselves because of the frustrated society in which they live.

scholarly journals Lake-level variability in Salar de Coipasa, Bolivia during the past ∼40,000 yr

2018 ◽  
Vol 91 (2) ◽  
pp. 881-891 ◽  
Author(s):  
J. Andrew Nunnery ◽  
Sherilyn C. Fritz ◽  
Paul A. Baker ◽  
Wout Salenbien
Keyword(s):  
Lake Level ◽  
Sediment Accumulation ◽  
Geochemical Data ◽  
South American ◽  
Climate History ◽  
Oxygen Isotope Stage ◽  
The Past ◽  
History Of ◽  
Diatom Stratigraphy ◽  
The Last Glacial

AbstractVarious paleoclimatic records have been used to reconstruct the hydrologic history of the Altiplano, relating this history to past variability of the South American summer monsoon. Prior studies of the southern Altiplano, the location of the world’s largest salt flat, the Salar de Uyuni, and its neighbor, the Salar de Coipasa, generally agree in their reconstructions of the climate history of the past ∼24 ka. Some studies, however, have highly divergent climatic records and interpretations of earlier periods. In this study, lake-level variation was reconstructed from a ∼14-m-long sediment core from the Salar de Coipasa. These sediments span the last ∼40 ka. Lacustrine sediment accumulation was apparently continuous in the basin from ∼40 to 6 ka, with dry or very shallow conditions afterward. The fossil diatom stratigraphy and geochemical data (δ13C, δ15N, %Ca, C/N) indicate fluctuations in lake level from shallow to moderately deep, with the deepest conditions correlative with the Heinrich-1 and Younger Dryas events. The stratigraphy shows a continuous lake of variable depth and salinity during the last glacial maximum and latter stages of Marine Oxygen Isotope Stage 3 and is consistent with environmental inferences and the original chronology of a drill core from Salar de Uyuni.

scholarly journals The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

2021 ◽  
Author(s):  
Kris A. Christensen ◽  
Eric B. Rondeau ◽  
Dionne Sakhrani ◽  
Carlo A. Biagi ◽  
Hollie Johnson ◽  
...  
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Chromosomal Polymorphism ◽  
Oncorhynchus Gorbuscha ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Temporal Isolation ◽  
History Of ◽  
Genome Assemblies ◽  
Salmon Fishery

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Sign in / Sign up

Export Citation Format

Share Document