A new era of mutation rate analyses: Concepts and methods

The mutation rate is a pivotal biological characteristic,intricately governed by natural selection and historically garnering considerable attention.Recent advances in high-throughput sequencing and analytical methodologies have profoundly transformed our understanding in this domain,ushering in an unprecedented era of mutation rate research.This paper aims to provide a comprehensive overview of the key concepts and methodologies frequently employed in the study of mutation rates.It examines various types of mutations,explores the evolutionary dynamics and associated theories,and synthesizes both classical and contemporary hypotheses.Furthermore,this review comprehensively explores recent advances in understanding germline and somatic mutations in animals and offers an overview of experimental methodologies,mutational patterns,molecular mechanisms,and driving forces influencing variations in mutation rates across species and tissues.Finally,it proposes several potential research directions and pressing questions for future investigations.

Rates and patterns of microsatellite mutations in common carp (Cyprinus carpio L.)

During genotyping 150 microsatellites in a F1 family of common carp, six mutations were found at five microsatellite loci. The overall mutation rate of common carp microsatellites was 2.53×10-4 per locus per generation. At five loci, mutations increased the length of alleles by at least one repeat unit, suggesting mutations at microsatellite loci in common carp do not follow strict stepwise mutation model. The data on mutation rates and patterns can facilitate population genetics studies, and provide useful parameters for estimating a long-term effective population size of common carp.

The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria

Mutation is a primary source of genetic variation that is used to power evolution.Many studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for survival.Using a mutation accumulation experiment,an unbiased method for mutation study,we found an extremely low base-substitution mutation rate of 5.94×10^(-11) per nucleotide site per cell division(95%Poisson confdence intervals:4.65×10^(-11),7.48×10^(-11))and indel mutation rate of 8.25×10^(-12) per site per cell division(95%confdence intervals:3.96×10^(-12),1.52×10^(-11))in the bacterium Photorhabdus luminescens ATCC29999.The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction.It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the efective population size(drift-barrier hypothesis)and we found that the efective population size of this bacterium is signifcantly greater than most other bacteria.This fnding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fdelity can evolve within organisms that maintain large efective population sizes.

Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history.Herein,we estimated the de novo mutation rate of pigs as 3.6×10-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation.Using this mutation rate,we re-investigated the evolutionary history of pigs.The estimated divergence time of~10 kiloyears ago(KYA)between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence.However,other divergence events inferred here were not as ancient as previously described.Our estimates suggest that Sus speciation occurred~1.36 million years ago(MYA);European wild pigs split from Asian wild pigs only~219 KYA;and south and north Chinese wild pigs split~25 KYA.Meanwhile,our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain,northern China,approximately 20 KYA,supporting the possibly independent domestication in northern China along the middle Yellow River.We also found that the maximum effective population size of pigs was~6 times larger than estimated before.An archaic migration from other Sus species originating~2 MYA to European pigs was detected during western colonization of pigs,which may affect the accuracy of previous demographic inference.Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

Study on γ-Ray Irradiation Mutation of Bacillus subtilis NCD-2

[Objective] To study the effect of 60Co γ-rays irradiation on Botrytis cinerea biocontrol strains—Bacillus subtilis NCD-2. [Method] NCD-2 cells were irradiated at different doses of γ-rays from 100 to 2 000 Gy. The strains were screened by plate confrontation method and Oxford cup diffusion. [Result] The curves of the relationship of irradiation dose and mutation and lethal rate were obtained. The results showed that lethal rate increased with the increasing of irradiation dose. The lethal rate of 1 000 Gy irradiation dose reached 99.50%. The mutation rate increased below 500 Gy and decreased above 500 Gy. The highest mutation rate occurred when the irradiation dose was between 400 and 700 Gy, and the average mutation rate was above 15%. The optimal irradiation dose was 500 Gy, when the average mutation rate was 26.51% and lethal rate was 77.71%. [Conclusion] This study provided references for γ-rays irradiation mutation of Bacillus subtilis.

Screening of Biocontrol Strain Bacillus subtilis by N^+ Ion Beam Implantation

[Objective] This study was to investigate the effect of N＋ ion beam implantation on the survival rate and mutation rate of biocontrol strain Bacillus subtilis. [Method] The factors influencing B. subtilis ion beam implantation, including culture time, dilution concentration, solvent, drying time of mycoderm were optimized. B. subtilis cells were implanted by using ion beam at dose of 2.0×10^14～4.0×10^14 ions/cm2 and the energy of 30 kev. Then the methods of culturing colonies confronting each other on plate and Oxford cup diffusion were used to screening strains. [Result] The optimal parameters were found as follows： culture in liquid for 20-24 h, dilution with sterile water to 106 cells/ml and drying time of 60 min for sample preparation; the optimal N＋ ion beam implantation dose of 2.0×10^14～4.0×10^14 ions/cm2 at the energy of 30 kev, the survival rate of 8.43%-26.71% and the mutation rate of 3.50%-5.43%. [Conclusion] This study provided reference for ion beam implantation mutation of B. subtilis.

Virtual reconfigurable architecture for evolving combinational logic circuits

A virtual reconfigurable architecture(VRA)-based evolvable hardware is proposed for automatic synthesis of combinational logic circuits at gate-level.The proposed VRA is implemented by a Celoxica RC1000 peripheral component interconnect(PCI)board with an Xilinx Virtex xcv2000E field programmable gate array(FPGA).To improve the quality of the evolved circuits,the VRA works through a two-stage evolution: finding a functional circuit and minimizing the number of logic gates used in a feasible circuit.To optimize the algorithm performance in the two-stage evolutionary process and set free the user from the time-consuming process of mutation parameter tuning,a self-adaptive mutation rate control(SAMRC)scheme is introduced.In the evolutionary process,the mutation rate control parameters are encoded as additional genes in the chromosome and also undergo evolutionary operations.The efficiency of the proposed methodology is tested with the evolutions of a 4-bit even parity function,a 2-bit multiplier,and a 3-bit multiplier.The obtained results demonstrate that our scheme improves the evolutionary design of combinational logic circuits in terms of quality of the evolved circuit as well as the computational effort,when compared to the existing evolvable hardware approaches.

ZIKA-How fast does this virus mutate?

The World Health Organization has declared the present Zika virus epidemic to be a ＇Public Health Emergency of International Concern＇. The virus appears to have spread from Thailand to French Polynesia in 2013, and has since infected over a million people in the countries of South and Central America. In most cases the infection is mild and transient, but the virus does appear to be strongly neurotropic and the presumptive cause of both birth defects in fetuses and Guillain-Barr6 syndrome in some adults. In this paper, the techniques and utilities developed in the study of mitochondrial DNA were applied to the Zika virus. As a result, it is possible to show in a simple manner how a phylogenetic tree may be constructed and how the mutation rate of the virus can be measured. The study showed the mutation rate to vary between 12 and 25 bases a year, in a viral genome of 10 272 bases. This rapid mutation rate will enable the geographic spread of the epidemic to be monitored easily and may also prove useful in assisting the identification of preventative measures that are working, and those that are not.

Mutation Studies of 31 Highly Mutated Y-chromosomal Short Tandem Repeat Systems in the Han Population of Northern China

A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats(Y-STRs)(DYS19,DYS390,DYS391,DYF399S1,DYF404S1,DYS439,DYS444,DYS449,DYS452,DYS456,DYS458,DYS460,DYS481,DYS508,DYS513,DYS516,DYS518,DYS543,DYS547,DYS549,DYS552,DYS557,DYS570,DYS576,DYS612,DYS622,DYS626,DYS627,DYS630,DYS635,and Y-GATA-A10)was developed for investigating the mutation rates of 31 highly mutated Y-STR genes in the Han population of northern China.The mutation rates of the 31 highly mutated Y-STRs were calculated using the father-son pair study method after typing 526 Northern Han father-son pairs with this system.Statistically,148 Y-STR mutations were found,with mutation rates ranging from 0(95%confidence interval[CI]0 to 9.0×10^(−3),DYS622)to 7.0×10^(−2)(95%CI 5.1×10^(−2)to 9.7×10^(−2),DYF399S1).Out of these,126 father-son pairs were successfully identified,with a distinction rate of 24.0%(95%CI 20.4%-27.9%).The ability of the 31 highly mutated Y-STRs to distinguish closely related males from the same paternal lineage in the Northern Han population is extremely valuable for criminal investigations and other purposes.

Developing controllable hypermutable Clostridium cells through manipulating its methyl-directed mismatch repair system

Development of controllable hypermutable cells can greatly benefit understanding and harnessing microbial evolution.However,there have not been any similar sys-tems developed for Clostridium,an important bacterial genus.Here we report a novel two-step strategy for de-veloping controllable hypermutable cells of Clostridium acetobutylicum,an important and representative indus-trial strain.Firstly,the mutS/L operon essential for methyl-directed mismatch repair(MMR)activity was inactivated from the genome of C.acetobutylicum to generate hy-permutable cells with over 250-fold increased mutation rates.Secondly,a proofreading control system carrying an inducibly expressed mutS/L operon was constructed.The hypermutable cells and the proofreading control system were integrated to form a controllable hypermut-able system SMBMutC,of which the mutation rates can be regulated by the concentration of anhydrotetracycline(aTc).Duplication of the miniPthl-tetR module of the proof-reading control system further signifi cantly expanded the regulatory space of the mutation rates,demonstrating hypermutable Clostridium cells with controllable mutation rates are generated.The developed C.acetobutylicum strain SMBMutC2 showed higher survival capacities than the control strain facing butanol-stress,indicating greatly increased evolvability and adaptability of the controllable hypermutable cells under environmental challenges.

How Often Does Human DNA Mutate?

Editor＇s comments The human mutation rate how often new changes appear in the DNA--is fundamental to understanding many aspects of medical genetics and human evolutionary genetics. But it is low, and has therefore been difficult to measure. In the past, scientists could only estimate it approximately, either by observing how often mutant phenotypes appeared, or by comparison of humans and closely related species, such as chimpanzee, where many mutations could accumulate but the time period was uncertain. Now, a new study supported by the NSFC in China and The Royal Society in the UK reports the first direct measurement of the human mutation rate at the individual letters （ nucleotides or bases） of DNA. This was possible because new （ next ）-generation sequencing technology is much more powerful than the methods available previously. The work was published in the lead- ing journal Currerzt Biology on 15th September 2009. The results were reported in the news by Nature, Science and the BBC , as well as in more than 20 Chinese newspapers and radio stations after the work first appeared online on 27th August. It was also one of the research highlights in Nature on 3rd September, which commented ＂ This direct measurement of the human mutation rate should help researchers to refine evolutionary dating and better understand the source of genetic disease＇. From the work, researchers could estimate that everyone has around 200 new mutations in their genome ; as the authors said, ＂we are all mutants＂. The ability to reliably measure rates of DNA mutation means we can begin to ask how mutation rates vary between different regions of the genome and perhaps also between different individuals.