scholarly journals Landscape of gene transposition-duplication within the Brassicaceae family

2017 ◽  
Author(s):  
Dong-Ha Oh ◽  
Maheshi Dassanayake
Keyword(s):  
Network Topology ◽  
Evolutionary History ◽  
Open Reading Frames ◽  
Gene Arrangement ◽  
Intergenic Sequence ◽  
Gene Transposition ◽  
History Of ◽  
Supplementary Text ◽  
Duplicated Loci ◽  
Evolutionary Paths

ABSTRACTWe developed the CLfinder-OrthNet pipeline that detects co-linearity in gene arrangement among multiple closely related genomes; find ortholog groups; and encodes the evolutionary history of each ortholog group into a representative network (OrthNet). Using a search based on network topology, out of a total of 17,432 OrthNets in six Brassicaceae genomes, we identified 1,394 that included gene transposition-duplication (tr-d) events in one or more genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. They also had a higher chance of being expressed and derived from older tr-d events. We also found an enrichment, compared to random chance, of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3. The CLfinder-OrthNet pipeline provides a flexible and a modular toolkit to compare gene order, encode and visualize evolutionary paths among orthologs as networks, and identify all gene loci that share the same evolutionary history using network topology searches.Funding source: This work was supported by National Science Foundation (MCB 1616827) and the Next Generation BioGreen21 Program (PJ011379) of the Rural Development Administration, Republic of Korea.Online-only Supplementary materials includes supplementary text (S1-S10), methods (M1-M4), figures (S1-S7), and tables (S1-S3), in two PDF files, one for text and methods and the other for figures and tables. Additionally, Supplementary Dataset S1 is available at the Figshare repository (https://doi.org/10.6084/m9.figshare.5825937) and Dataset S2 and S3 as separate Excel files.

scholarly journals Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jiguang Wang ◽  
Hossein Khiabanian ◽  
Davide Rossi ◽  
Giulia Fabbri ◽  
Valter Gattei ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Evolutionary History ◽  
Directed Graphs ◽  
Evolutionary Process ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Cross Sectional ◽  
History Of ◽  
Evolutionary Paths ◽  
Clonal Replacement

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

scholarly journals Evolutionary history of mitochondrial genomes in Discoba, including the extreme halophile Pleurostomum flabellatum (Heterolobosea)

2020 ◽  
Author(s):  
Khaoula Ettahi ◽  
Duck Hyun Lhee ◽  
Ji Yeon Sung ◽  
Alastair G B Simpson ◽  
Jong Soo Park ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Genome ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Transport Chain ◽  
Circular Molecule ◽  
History Of ◽  
Extreme Habitats ◽  
Genome Information ◽  
Naegleria Gruberi

Abstract Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), since this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829 bp long circular molecule, including 40 CDSs (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and N. fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved-oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

STRUCTURAL REARRANGEMENTS AT THE REGULATORY REGION OF THE DRAS1 GENE IN THE EVOLUTIONARY HISTORY OF PHYLOGENETICALLY DISTANT DROSOPHILA SPECIES

2018 ◽  
Author(s):  
A.I. CHEKUNOVA ◽  
◽  
S. YU. SOROKINA ◽  
E.A. SIVOPLYAS ◽  
G.N. BAKHTOYAROV ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Regulatory Region ◽  
Drosophila Species ◽  
Structural Rearrangements ◽  
History Of
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