scholarly journals Genomes: At the edge of chaos with maximum information capacity

2016 ◽  
Vol 30 (02) ◽  
pp. 1550255
Author(s):  
Sing-Guan Kong ◽  
Hong-Da Chen ◽  
Andrew Torda ◽  
H. C. Lee
Keyword(s):  
Base Composition ◽  
Narrow Range ◽  
Index Formula ◽  
Neutral Evolution ◽  
Sequence Length ◽  
Infinite Length ◽  
Genome Sequences ◽  
Maximum Information ◽  
Edge Of Chaos ◽  
Complete Genomic

We propose an order index, [Formula: see text], which quantifies the notion of “life at the edge of chaos” when applied to genome sequences. It maps genomes to a number from 0 (random and of infinite length) to 1 (fully ordered) and applies regardless of sequence length and base composition. The 786 complete genomic sequences in GenBank were found to have [Formula: see text] values in a very narrow range, 0.037 ± 0.027. We show this implies that genomes are halfway towards being completely random, namely, at the edge of chaos. We argue that this narrow range represents the neighborhood of a fixed-point in the space of sequences, and genomes are driven there by the dynamics of a robust, predominantly neutral evolution process.

scholarly journals Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
D Libkind ◽  
N Čadež ◽  
D A Opulente ◽  
Q K Langdon ◽  
C A Rosa ◽  
...  
Keyword(s):  
Sexual Behaviors ◽  
Yeast Species ◽  
Novel Species ◽  
Genetic Distances ◽  
Biological Research ◽  
Genome Sequences ◽  
Novel Taxa ◽  
Bioinformatic Approaches ◽  
Species Descriptions ◽  
Complete Genomic

ABSTRACT In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.

scholarly journals Complete Genome Sequences of Seven New Chrysodeixis includens Nucleopolyhedrovirus Isolates from Minas Gerais and Mato Grosso States in Brazil

2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Saluana R. Craveiro ◽  
Peter W. Inglis ◽  
Laura Lisieux S. Monteiro ◽  
Luis Arthur V. M. Santos ◽  
Roberto C. Togawa ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Southeastern Brazil ◽  
Genome Sequences ◽  
Mato Grosso ◽  
Content Type ◽  
Soybean Looper ◽  
Reading Frames ◽  
Viral Isolates ◽  
Chrysodeixis Includens ◽  
Complete Genomic

We report the complete genomic sequences of seven viral isolates from the soybean looper (Chrysodeixis includens) from midwestern and southeastern Brazil. The genomes range from 138,760 to 139,637 bp in length with a G+C content of 39.2% and 140 open reading frames (ORFs).

scholarly journals Genome Sequences of SAT 2 Foot-and-Mouth Disease Viruses from Egypt and Palestinian Autonomous Territories (Gaza Strip)

2012 ◽  
Vol 86 (16) ◽  
pp. 8901-8902 ◽  
Author(s):  
Begoña Valdazo-González ◽  
Nick J. Knowles ◽  
Jef Hammond ◽  
Donald P. King
Keyword(s):  
Middle East ◽  
North Africa ◽  
Gaza Strip ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Sahara Desert ◽  
Genome Sequences ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Complete Genomic

Two foot-and-mouth disease virus (FMDV) genome sequences have been determined for isolates collected from recent field outbreaks in North Africa (Egypt) and the Middle East (Palestinian Autonomous Territories). These data represent the first examples of complete genomic sequences for the FMDV SAT 2 topotype VII, which is thought to be endemic in countries immediately to the south of the Sahara desert. Further studies are now urgently required to provide insights into the epidemiological links between these outbreaks and to define the pathogenicity of this emerging lineage.

scholarly journals DNAskew: Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

2004 ◽  
Vol 36 (1) ◽  
pp. 16-20 ◽  
Author(s):  
Xiang-Ru Ma ◽  
Shao-Bo Xiao ◽  
Ai-Zhen Guo ◽  
Jian-Qiang Lü ◽  
Huan-Chun Chen
Keyword(s):  
Statistical Analysis ◽  
Base Composition ◽  
Script Language ◽  
Genome Sequences ◽  
Strand Asymmetry ◽  
Rule Type ◽  
Codon Composition ◽  
Dna Strands ◽  
Phylogenetic Evolution ◽  
Relationship Of

Abstract Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

scholarly journals Insertions and deletions in the RNA sequence–structure map

2021 ◽  
Vol 18 (183) ◽  
Author(s):  
Nora S. Martin ◽  
Sebastian E. Ahnert
Keyword(s):  
Structural Changes ◽  
Structural Effect ◽  
Neutral Evolution ◽  
Sequence Length ◽  
Sequence Structure ◽  
Rna Sequences ◽  
Genetic Changes ◽  
Insertions And Deletions ◽  
Phenotypic Robustness ◽  
Nucleotide Insertions

Genotype–phenotype maps link genetic changes to their fitness effect and are thus an essential component of evolutionary models. The map between RNA sequences and their secondary structures is a key example and has applications in functional RNA evolution. For this map, the structural effect of substitutions is well understood, but models usually assume a constant sequence length and do not consider insertions or deletions. Here, we expand the sequence–structure map to include single nucleotide insertions and deletions by using the RNAshapes concept. To quantify the structural effect of insertions and deletions, we generalize existing definitions for robustness and non-neutral mutation probabilities. We find striking similarities between substitutions, deletions and insertions: robustness to substitutions is correlated with robustness to insertions and, for most structures, to deletions. In addition, frequent structural changes after substitutions also tend to be common for insertions and deletions. This is consistent with the connection between energetically suboptimal folds and possible structural transitions. The similarities observed hold both for genotypic and phenotypic robustness and mutation probabilities, i.e. for individual sequences and for averages over sequences with the same structure. Our results could have implications for the rate of neutral and non-neutral evolution.

scholarly journals Identifying branch-specific positive selection throughout the regulatory genome using an appropriate neutral proxy

2019 ◽  
Author(s):  
Alejandro Berrio ◽  
Ralph Haygood ◽  
Gregory A Wray
Keyword(s):  
Positive Selection ◽  
Regulatory Elements ◽  
Directional Selection ◽  
Neutral Evolution ◽  
Sequence Length ◽  
Open Chromatin ◽  
Sequence Alignments ◽  
Noncoding Dna ◽  
Region Length ◽  
The Impact

AbstractAdaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. Here, we introduce a method we called adaptyPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome. We use ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We apply the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. We also simulate sequence alignments under different classes of evolution in order to validate the ability of adaptiPhy to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we evaluate the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity.

scholarly journals Complete Genomic Sequences of Three Salmonella enterica subsp. enterica Serovar Muenchen Strains from an Orchard in San Joaquin County, California

2020 ◽  
Vol 9 (13) ◽  
Author(s):  
Thao D. Tran ◽  
Steven Huynh ◽  
Craig T. Parker ◽  
Robert Hnasko ◽  
Lisa Gorski ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Complete Genome ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Content Type ◽  
San Joaquin County ◽  
Complete Genomic

We present here the complete genome sequences of three Salmonella enterica subsp. enterica serovar Muenchen strains, LG24, LG25, and LG26. All three strains were isolated from almond drupes grown in an orchard in San Joaquin County, California, in 2016. These genomic sequences are nonidentical and will contribute to our understanding of S. enterica genomics.

Neutral Evolution of Synonymous Base Composition in the Brassicaceae

2006 ◽  
Vol 64 (1) ◽  
pp. 136-141 ◽  
Author(s):  
Stephen I. Wright ◽  
Gabriel Iorgovan ◽  
Sushant Misra ◽  
Mohammad Mokhtari
Keyword(s):  
Base Composition ◽  
Neutral Evolution

scholarly journals Metagenomic Analysis of Cucumber RNA from East Timor Reveals an Aphid lethal paralysis virus Genome

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
Solomon Maina ◽  
Owain R. Edwards ◽  
Luis de Almeida ◽  
Abel Ximenes ◽  
Roger A. C. Jones
Keyword(s):  
United States ◽  
South Africa ◽  
The United States ◽  
Virus Genome ◽  
East Timor ◽  
Chinese Isolate ◽  
Cucumber Plant ◽  
Genome Sequences ◽  
Paralysis Virus ◽  
Complete Genomic

ABSTRACT We present here the first complete genomic Aphid lethal paralysis virus (ALPV) sequence isolated from cucumber plant RNA from East Timor. We compare it with two complete ALPV genome sequences from China, and one each from Israel, South Africa, and the United States. It most closely resembled the Chinese isolate LGH genome.

Sign in / Sign up

Export Citation Format

Share Document