Acetic acid-and furfural-based adaptive evolution of Saccharomyces cerevisiae strains for improving stress tolerance and lignocellulosic ethanol production

Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae strains.Development of industrial S.cerevisiae strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol production.In this study,the acetic acid or furfural tolerance of different S.cerevisiae strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress conditions.The acetic acid-based adaptive strain SPSC01-TA9 produced 30.5 g·L^(-1)ethanol with a yield of 0.46 g·g^(-1)in the presence of 9 g·L^(-1)acetic acid,while the acetic acid/furfural-based adaptive strain SPSC01-TAF94 produced more ethanol of 36.2 g·L^(-1)with increased yield up to 0.49 g·g^(-1)in the presence of both 9 g·L^(-1)acetic acid and 4 g·L^(-1)furfural.Significant improvements were also observed during non-detoxified corn stover hydrolysate culture by SPSC01-TAF94,which achieved ethanol production and yield of 29.1 g·L^(-1)and 0.49 g·g^(-1),respectively,the growth and fermentation efficiency of acetic acid/furfural-based adaptive strain in hydrolysate was 95%higher than those of wildtype strains,indicating the acetic acid-and furfural-based adaptive evolution strategy could be an effective approach for improving lignocellulosic ethanol production.The adapted strains developed in this study with enhanced tolerance against acetic acid and furfural could be potentially contribute to economically feasible and sustainable lignocellulosic biorefinery.

Genomics and morphometrics reveal the adaptive evolution of pikas

Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81specimens, representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa,Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other pikas.Consistently, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearingrelated genes. Analysis of shared amino acid substitutions and positively selected genes(PSGs) in Alienauroa and Ochotona identified two genes, i.e.,mitochondrial function-related TSFM(p.Q155E) and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments(e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.

Adaptive evolution of rbcL in Reaumuria soon garica(Tamaricaceae)

In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.

Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection

Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.

Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits

Actinidia arguta,the most widely distributed Actinidia species and the second cultivated species in the genus,can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit,rapid softening,and excellent cold tolerance.Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear.Here,we generated a chromosome-scale genome assembly of an autotetraploid male A.arguta accession.The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes.Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups,Southern and Northern,which first diverged 12.9 million years ago.A.arguta underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late Pleistocene.Population genomics studies using paleoclimate data enabled us to discern the evolution of the species’adaptation to different historical environments.Three genes(AaCEL1,AaPME1,and AaDOF1)related to flesh softening were identified by multi-omics analysis,and their ability to accelerate flesh softening was verified through transient expression assays.A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome(Chr3)or autosomal chromosomes showed biased expression during stamen or carpel development.This chromosome-level assembly of the autotetraploid A.arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A.arguta.

Adaptive evolution of scn4aa in Takifugu and Tetraodon

Tetrodotoxin(TTX)is a potent neurotoxin firstly discovered in the ovary of pufferfish.The genetic basis of voltage-gated sodium channel resistance to TTX has been widely studied,but it remains unclear in the evolution history of voltage-gated sodium channel resistance to TTX in pufferfish with different TTX concentrations.In this study,six scn4aa coding sequences of pufferfish were firstly cloned and sequenced,then used to investigate the adaptive evolution of scn4aa associated with TTX concentration and reconstruct ancestral sequences with seven scn4aa of other fishes.The result of CODEML(codon substitution model)program from the PAML(phylogenetic analysis by maximum likelihood)package shows only in the genus of Takifugu,which contains TTX highly in the liver,under positive selection.The result also indicates that three of four positively selected sites are located in the intracellular regions,which may compensate for normal function.The ancestral sequence reconstruction may suggest that the replacements providing weak toxin resistance might have appeared first in scn4aa,then the genus Takifugu evolved stronger resistance to TTX later.These results contribute to the explanation of the evolutional history of voltage-gated sodium channel resistance to TTX in pufferfish.

Operational optimization of copper flotation process based on the weighted Gaussian process regression and index-oriented adaptive differential evolution algorithm

Concentrate copper grade(CCG)is one of the important production indicators of copper flotation processes,and keeping the CCG at the set value is of great significance to the economic benefit of copper flotation industrial processes.This paper addresses the fluctuation problem of CCG through an operational optimization method.Firstly,a density-based affinity propagationalgorithm is proposed so that more ideal working condition categories can be obtained for the complex raw ore properties.Next,a Bayesian network(BN)is applied to explore the relationship between the operational variables and the CCG.Based on the analysis results of BN,a weighted Gaussian process regression model is constructed to predict the CCG that a higher prediction accuracy can be obtained.To ensure the predicted CCG is close to the set value with a smaller magnitude of the operation adjustments and a smaller uncertainty of the prediction results,an index-oriented adaptive differential evolution(IOADE)algorithm is proposed,and the convergence performance of IOADE is superior to the traditional differential evolution and adaptive differential evolution methods.Finally,the effectiveness and feasibility of the proposed methods are verified by the experiments on a copper flotation industrial process.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species interaction.As the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning.In this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and coevolution.Firstly,we focused on the adaptive evolution of morphological,behavioral,and physiological traits.Secondly,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence mechanisms.Thirdly,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and competition.Overall,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies.Finally,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into Its Adaptive Evolution in Tropical Desert

Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

Population genome of the newly discovered Jinchuan yak to understand its adaptive evolution in extreme environments and generation mechanism of the multirib trait

The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive evolution.The recently discovered Jinchuan yak population has many individuals with multiple ribs.However,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib trait.Here,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 individuals.Population genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic yak.Combined with geological change,the Jinchuan yak’s evolutionary origin is speculated to be about 6290 years ago,which may be related to the unique geographical environment of the eastern edge of the QTP during this period.Compared with other domestic yaks,this new population has 280 positively selected genes.The genes related to skeletal function hold a considerable and remarkable proportion,suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau environment.The genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib trait.Our findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.

Adaptive Evolution of cry Genes in Bacillus thuringiensis:Implications for Their Specificity Determination

The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific activity against only one or a few insect species. Extensive studies are mostly focusing on the structural and functional relationships of Cry proteins, and have revealed several residues or domains that are important for the target recognition and receptor attachment. In this study, we have employed a maximum likelihood method to detect evidence of adaptive evolution in Cry proteins, and have identified 24 positively selected residues, which are all located in Domain Ⅱ or Ⅲ. Combined with known data from mutagenesis studies, the majority of these residues, at the molecular level, contribute much to the insect specificity determination. We postulate that the potential pressures driving the diversification of Cry proteins may be in an attempt to adapt for the ＂arm race＂ between δ-endotoxins and the targeted insects, or to enlarge their target spectra, hence result in the functional divergence. The sites identified to be under positive selection would provide targets for further structural and functional analyses on Cry proteins.

Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing:a Bayesian population structure and phylogenetic study

Background:Beijing sub-pedigree 2(BSP2)and T sub-lineage 6(TSL6)are two clades belonging to Beijing and T family of Mycobacterium tuberculosis(MTB),respectively,defined by Bayesian population structure analysis based on 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats(MIRU-VNTR).Globally,over 99%of BSP2 and 89%of TSL6 isolates were distributed in Chongqing,suggesting their possible local adaptive evolution.The objective of this paper is to explore whether BSP2 and TSL6 originated by their local adaptive evolution from the specific isolates of Beijing and T families in Chongqing.Methods:The genotyping data of 16090 MTB isolates were collected from laboratory collection,published literatures and SITVIT database before subjected to Bayesian population structure analysis based on 24-loci MIRUVNTR.Spacer Oligonucleotide Forest(Spoligoforest)and 24-loci MIRU-VNTR-based minimum spanning tree(MST)were used to explore their phylogenetic pathways,with Bayesian demographic analysis for exploring the recent demographic change of TSL6.Results:Phylogenetic analysis suggested that BSP2 and TSL6 in Chongqing may evolve from BSP4 and TSL5,respectively,which were locally predominant in Tibet and Jiangsu,respectively.Spoligoforest showed that Beijing and T families were genetically distant,while the convergence of the MIRU-VNTR pattern of BSP2 and TSL6 was revealed by WebLogo.The demographic analysis concluded that the recent demographic change of TSL6 might take 111.25 years.Conclusions:BSP2 and TSL6 clades might originate from BSP4 and TSL5,respectively,by their local adaptive evolution in Chongqing.Our study suggests MIRU-VNTR be combined with other robust markers for a more comprehensive genotyping approach,especially for families of clades with the same MIRU-VNTR pattern.

An Enhanced Adaptive Differential Evolution Approach for Constrained Optimization Problems

Effective constrained optimization algorithms have been proposed for engineering problems recently.It is common to consider constraint violation and optimization algorithm as two separate parts.In this study,a pbest selection mechanism is proposed to integrate the current mutation strategy in constrained optimization problems.Based on the improved pbest selection method,an adaptive differential evolution approach is proposed,which helps the population jump out of the infeasible region.If all the individuals are infeasible,the top 5%of infeasible individuals are selected.In addition,a modified truncatedε-level method is proposed to avoid trapping in infeasible regions.The proposed adaptive differential evolution approach with an improvedεconstraint processmechanism(IεJADE)is examined on CEC 2006 and CEC 2010 constrained benchmark function series.Besides,a standard IEEE-30 bus test system is studied on the efficiency of the IεJADE.The numerical analysis verifies the IεJADE algorithm is effective in comparisonwith other effective algorithms.

An improved adaptive differential evolution algorithm for single unmanned aerial vehicle multitasking

Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.

Identification of genes involved in cadmium-ion tolerance in evolutionary Synechocystis sp.PCC 6803 tolerant to both cadmium and high light

Photosynthetic cyanobacteria have shown great potential as“autotrophic cell factories”for the synthesis of fuels and chemicals.However,poor tolerance to various environmental stressors such as high light and heavy metals is an important factor limiting their economic viability.While numerous studies have focused on the tolerance mechanism of cyanobacteria to individual stressors,their response to simultaneous stresses remains to be recovered.To investigate the mechanism of cross tolerance to heavymetal Cd^(2+) and high light,the model cyanobacterium Synechocystis sp.PCC 6803 tolerant to both Cd^(2+) and high light was obtained via about 800 days’cross-adaptive laboratory evolution.Three evolutionary strains capable of tolerating both 5.5 μmol·L^(-1) Cd^(2+) and 600 μmol·m^(-2)·s^(-1) high light were successfully obtained,achieving about 83%enhancement of Cd^(2+) tolerance compared with the parent strain.The different response of parent and evolutionary strains to Cd^(2+) was elucidated via metabolomics.Furthermore,a total of 15 genes that were mutated during evolution were identified by whole-genome re-sequencing.Finally,by single-gene knockout and complementation analysis,four genes including ssl2615,sll1732,ssr1480,and sll1659 involved in the improvement of Cd^(2+) tolerance under high-light condition were successfully identified.This work explored the tolerance mechanism of Synechocystis sp.PCC 6803 to cadmium under high-light condition and provided valuable reference for deciphering multitolerance mechanism of cyanobacteria in the future.

Evolutionary implications of Avian Infectious Bronchitis Virus(AIBV)analysis

For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.

Identification of genes under positive selection reveals evolutionary adaptation of Ulva mutabilis

Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.

Leaf nitrogen and phosphorus are more sensitive to environmental factors in dicots than in monocots,globally

Leaf nitrogen(N)and phosphorus(P)levels provide critical strategies for plant adaptions to changing environments.However,it is unclear whether leaf N and P levels of different plant functional groups(e.g.,monocots and dicots)respond to environmental gradients in a generalizable pattern.Here,we used a global database of leaf N and P to determine whether monocots and dicots might have evolved contrasting strategies to balance N and P in response to changes in climate and soil nutrient availability.Specifically,we characterized global patterns of leaf N,P and N/P ratio in monocots and dicots,and explored the sensitivity of stoichiometry to environment factors in these plants.Our results indicate that leaf N and P levels responded to environmental factors differently in monocots than in dicots.In dicots,variations of leaf N,P and N/P ratio were significantly correlated to temperature and precipitation.In monocots,leaf N/P ratio was not significantly affected by temperature or precipitation.This indicates that leaf N,P and N/P ratio are less sensitive to environmental dynamics in monocots.We also found that in both monocots and dicots N/P ratios are associated with the availability of soil total P rather than soil total N,indicating that P limitation on plant growth is pervasive globally.In addition,there were significant phylogenetic signals for leaf N(λ=0.65),P(λ=0.57)and N/P ratio(λ=0.46)in dicots,however,only significant phylogenetic signals for leaf P in monocots.Taken together,our findings indicate that monocots exhibit a“conservative”strategy(high stoichiometric homeostasis and weak phylogenetic signals in stoichiometry)to maintain their growth in stressful conditions with lower water and soil nutrients.In contrast,dicots exhibit lower stoichiometric homeostasis in changing environments because of their wide climate-soil niches and significant phylogenetic signals in stoichiometry.

EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp(Litopenaeus vannamei)

Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.

A New Model for Network Security Situation Assessment of the Industrial Internet

To address the problem of network security situation assessment in the Industrial Internet,this paper adopts the evidential reasoning(ER)algorithm and belief rule base(BRB)method to establish an assessment model.First,this paper analyzes the influencing factors of the Industrial Internet and selects evaluation indicators that contain not only quantitative data but also qualitative knowledge.Second,the evaluation indicators are fused with expert knowledge and the ER algorithm.According to the fusion results,a network security situation assessment model of the Industrial Internet based on the ER and BRB method is established,and the projection covariance matrix adaptive evolution strategy(P-CMA-ES)is used to optimize the model parameters.This method can not only utilize semiquantitative information effectively but also use more uncertain information and prevent the problem of combinatorial explosion.Moreover,it solves the problem of the uncertainty of expert knowledge and overcomes the problem of low modeling accuracy caused by insufficient data.Finally,a network security situation assessment case of the Industrial Internet is analyzed to verify the effectiveness and superiority of the method.The research results showthat this method has strong applicability to the network security situation assessment of complex Industrial Internet systems.It can accurately reflect the actual network security situation of Industrial Internet systems and provide safe and reliable suggestions for network administrators to take timely countermeasures,thereby improving the risk monitoring and emergency response capabilities of the Industrial Internet.