scholarly journals Genetic equidistance at the nucleotide level

2017 ◽  
Author(s):  
Dejian Yuan ◽  
Shi Huang
Keyword(s):  
Dna Sequences ◽  
Ad Hoc ◽  
Nucleotide Level ◽  
Complex Species ◽  
Molecular Clock Hypothesis ◽  
Primary Determinant ◽  
Outgroup Taxon ◽  
Clock Hypothesis ◽  
Genetic Equidistance ◽  
Acid Percentage

AbstractThe genetic equidistance phenomenon was first discovered in 1963 by Margoliash and shows complex taxa to be all approximately equidistant to a less complex species in amino acid percentage identity. The result has been mis-interpretated by the ad hoc universal molecular clock hypothesis, and the much overlooked mystery was finally solved by the maximum genetic diversity hypothesis (MGD). Here, we studied 15 proteomes and their coding DNA sequences (CDS) to see if the equidistance phenomenon also holds at the CDS level. We performed DNA alignments for a total of 5 groups with 3 proteomes per group and found that in all cases the outgroup taxon was equidistant to the two more complex taxa species at the DNA level. Also, when two sister taxa (snake and bird) were compared to human as the outgroup, the more complex taxon bird was closer to human, confirming species complexity rather than time to be the primary determinant of MGD. Finally, we found the fraction of overlap sites where coincident substitutions occur to be inversely correlated with CDS conservation, indicating saturation to be more common in less conserved DNAs. These results establish the genetic equidistance phenomenon to be universal at the DNA level and provide additional evidence for the MGD theory.

scholarly journals The Genetic Equidistance Phenomenon at the Proteomic Level

2015 ◽  
Author(s):  
Denghui Luo ◽  
Shi Huang
Keyword(s):  
Molecular Clock ◽  
Ad Hoc ◽  
Neutral Theory ◽  
Maximum Distance ◽  
Complex Species ◽  
Molecular Clock Hypothesis ◽  
First Results ◽  
Small Set ◽  
Clock Hypothesis ◽  
Genetic Equidistance

The field of molecular evolution started with the alignment of a few protein sequences in the early 1960s. Among the first results found, the genetic equidistance result has turned out to be the most unexpected. It directly inspired the ad hoc universal molecular clock hypothesis that in turn inspired the neutral theory. Unfortunately, however, what is only a maximum distance phenomenon was mistakenly transformed into a mutation rate phenomenon and became known as such. Previous work studied a small set of selected proteins. We have performed proteome wide studies of 7 different sets of proteomes involving a total of 15 species. All 7 sets showed that within each set of 3 species the least complex species is approximately equidistant in average proteome wide identity to the two more complex ones. Thus, the genetic equidistance result is a universal phenomenon of maximum distance. There is a reality of constant albeit stepwise or discontinuous increase in complexity during evolution, the rate of which is what the original molecular clock hypothesis is really about. These results provide additional lines of evidence for the recently proposed maximum genetic diversity (MGD) hypothesis.

An evaluation of the molecular clock hypothesis using mammalian DNA sequences

1987 ◽  
Vol 25 (4) ◽  
pp. 330-342 ◽  
Author(s):  
Wen-Hsiung Li ◽  
Masako Tanimura ◽  
Paul M. Sharp
Keyword(s):  
Molecular Clock ◽  
Dna Sequences ◽  
Molecular Clock Hypothesis ◽  
Clock Hypothesis

scholarly journals You're one in a googol: optimizing genes for protein expression

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Mark Welch ◽  
Alan Villalobos ◽  
Claes Gustafsson ◽  
Jeremy Minshull
Keyword(s):  
Protein Expression ◽  
Dna Sequences ◽  
Ad Hoc ◽  
Protein Coding ◽  
Vast Number ◽  
Coding Sequences ◽  
Affect Expression ◽  
Continue Work ◽  
Existing Data ◽  
Rational Sequence

A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.

scholarly journals Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

2016 ◽  
Vol 54 (11) ◽  
pp. 2804-2812 ◽  
Author(s):  
Abdelmounaim Mouhajir ◽  
Olivier Matray ◽  
Sandrine Giraud ◽  
Laurent Mély ◽  
Christophe Marguet ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Species Complex ◽  
Pcr Amplification ◽  
Patient Specific ◽  
Molecular Evidence ◽  
Repetitive Dna Sequences ◽  
Complex Species ◽  
Content Type

The aim of this work was to document molecular epidemiology of Rasamsonia argillacea species complex isolates from cystic fibrosis (CF) patients. In this work, 116 isolates belonging to this species complex and collected from 26 CF patients and one patient with chronic granulomatous disease were characterized using PCR amplification assays of repetitive DNA sequences and electrophoretic separation of amplicons (rep-PCR). Data revealed a clustering consistent with molecular species identification. A single species was recovered from most patients. Rasamsonia aegroticola was the most common species, followed by R. argillacea sensu stricto and R. piperina , while R. eburnea was not identified. Of 29 genotypes, 7 were shared by distinct patients while 22 were patient specific. In each clinical sample, most isolates exhibited an identical genotype. Genotyping of isolates recovered from sequential samples from the same patient confirmed the capability of R. aegroticola and R. argillacea isolates to chronically colonize the airways. A unique genotype was recovered from two siblings during a 6-month period. In the other cases, a largely dominant genotype was detected. Present results which support the use of rep-PCR for both identification and genotyping for the R. argillacea species complex provide the first molecular evidence of chronic airway colonization by these fungi in CF patients.

scholarly journals Genetic equidistance at nucleotide level

Genomics ◽  
2017 ◽  
Vol 109 (3-4) ◽  
pp. 192-195 ◽  
Author(s):  
Dejian Yuan ◽  
Shi Huang
Keyword(s):  
Nucleotide Level ◽  
Genetic Equidistance
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