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adaptive evolution of cry Genes in Bacillus thuringiensis:Implications for Their Specificity Determination

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Genomics, Proteomics & Bioinformatics 2007年第2期5卷 102-110页

作者： Jin-Yu Wu Fang-Qing Zhao Jie Bai Gang Deng Song Qin Qi-Yu Bao Institute of Biomedical Informatics Wenzhou Medical College Wenzhou 325000 China Insititute of Oceanology Chinese Academy of Sciences Qingdao 266071 China.

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.

关键词： adaptive evolution Bacillus thuringiensis Cry protein maximum likelihood method

Genomic Mutations Within the Host Microbiome: adaptive evolution or Purifying Selection

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Engineering 2023年第1期20卷 96-102页

作者： Jiachao Zhang Rob Knight School of Food Science and Engineering Hainan UniversityHaikou 570228China Department of Pediatrics University of California San DiegoLa JollaCA 92093USA Center for Microbiome Innovation Jacobs School of EngineeringUniversity of California San DiegoLa JollaCA 92093USA Department of Bioengineering University of California San DiegoLa JollaCA 92093USA Department of Computer Science and Engineering University of California San DiegoLa JollaCA 92093USA

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.

关键词： Gut microbiota Genomic mutations adaptive evolution Purifying selection Single-nucleoti de variants

adaptive evolution of rbcL in Reaumuria soon garica(Tamaricaceae)

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Research in Cold and Arid Regions 2017年第1期9卷 78-88页

作者： ChaoJu Qian MengHe Gu HengXia Yin Yong Shi ChengLiang Yin Xia Yan XiaoFei Ma Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions Gansu ProvinceDepartment of Ecology and Agriculture ResearchNorthwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhouGansu 730000China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Desert and Desertification Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhouGansu 730000China Key Laboratory of Eco-hydrology and of Inland River Basin Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhouGansu 730000China

In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.***.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.

关键词： rbcL gene Reaumuria soongarica] Tamaricaceae adaptive evolution

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

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Chinese Journal of Chemical Engineering 2024年第8期72卷 26-33页

作者： Omama Rehman Youduo Wu Quan Zhang Jin Guo Cuihuan Sun Huipeng Gao Yaqing Xu Rui Xu Ayesha Shahid Chuang Xue State Key Laboratory of Fine Chemicals Frontiers Science Centre for Smart Materials Oriented Chemical EngineeringEngineering Research Center of Application and Transformation for Synthetic BiologySchool of BioengineeringDalian University of TechnologyDalian 116024China Ningbo Institute of Dalian University of Technology Ningbo 315016China SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co. Ltd.Dalian 116041China Microbial Research Institute of Liaoning Province Chaoyang 122000China Yunnan Provincial Rural Energy Engineering Key Laboratory Kunming 650600China US-Pak Center for Advanced Studies in Agriculture and Food Security University of AgricultureFaisalabadPakistan

Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol *** negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae *** of industrial *** strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol *** this study,the acetic acid or furfural tolerance of different *** strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress *** 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)*** 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 *** 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.

关键词： Saccharomyces cerevisiae Lignocellulosic ethanol production adaptive evolution Acetic acid Furfural

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

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 42-59页

作者： Jianjun Lu Cheng Pan Wei Fan Wanfei Liu Huayan Zhao Donghai Li Sen Wang Lianlian Hu Bing He Kun Qian Rui Qin Jue Ruan Qiang Lin Shiyou Lü Peng Cui CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China University of Chinese Academy of Sciences Beijing 100049China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 434200China

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 *** 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,*** 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 *** variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision ***,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme *** 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.

关键词： Ricinus communis L. adaptive evolution Selection signature Genetic variation Genome assembly

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

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Integrative Zoology 2021年第5期16卷 685-695页

作者： Daoliang LAN Wenhui JI Xianrong XIONG Qiqi LIANG Wenye YAO Tserang-Donko MIPAM Jincheng ZHONG Jian LI Ministry of Education of Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource and Utilization Southwest Minzu UniversityChengduChina Institute of Qinghai-Tibetan Plateau Southwest Minzu UniversityChengduChina Novogene Bioinformatics Institute BeijingChina

The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive *** recently discovered Jinchuan yak population has many individuals with multiple ***,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib ***,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 *** genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic *** 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 *** with other domestic yaks,this new population has 280 positively selected *** 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 *** genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib *** 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.

关键词： adaptive evolution genetic mechanism multirib trait Qinghai-Tibet Plateau yak

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

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Plant Communications 2024年第6期5卷 173-192页

作者： Xue-Mei Lu Xiao-Fen Yu Guo-Qiang Li Ming-Hao Qu Huan Wang Chuang Liu Yu-Ping Man Xiao-Han Jiang Mu-Zi Li Jian Wang Qi-Qi Chen Rui Lei Cheng-Cheng Zhao Yun-Qiu Zhou Zheng-Wang Jiang Zuo-Zhou Li Shang Zheng Chang Dong Bai-Lin Wang Yan-Xiang Sun Hui-Qin Zhang Jie-Wei Li Quan-Hui Mo Ying Zhang Xin Lou Hai-Xu Peng Ya-Ting Yi He-Xin Wang Xiu-Jun Zhang Yi-Bo Wang Dan Wang Li Li Qiong Zhang Wen-Xia Wang Yongbo Liu Lei Gao Jin-Hu Wu Yan-Chang Wang CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhanHubeiChina Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhouGansuChina College of Life Sciences University of Chinese Academy of SciencesBeijingChina Wuhan Frasergen Bioinformatics Co. LtdWuhanHubeiChina Institute of Soil and Fertilizer Anhui Academy of Agricultural SciencesHefeiChina College of Agricultural Sciences Xichang UniversityXichangSichuanChina Department of Horticulture Heilongjiang Academy of Agricultural SciencesHarbinHeilongjiangChina College of Life Sciences Langfang Normal UniversityLangfangHebeiChina Institute of Horticulture Zhejiang Academy of Agricultural SciencesHangzhouZhejiangChina Guangxi Institute of Botany Chinese Academy of SciencesGuilinGuangxiChina Xi’an Botanical Garden of Shaanxi Province Institute of Botany of Shaanxi ProvinceXi’anShaanxiChina Institute of Modern Agricultural Research Dalian UniversityDalianLiaoningChina Bioinformatics Center College of Plant Science and TechnologyBeijing University of AgricultureBeijingChina College of Agriculture Eastern Liaoning UniversityDandongLiaoningChina Dalian Institute of Chemical Physics Chinese Academy of SciencesDalianLiaoningChina State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijingChina Hubei Hongshan Laboratory WuhanHubeiChina The New Zealand Institute for Plant and Food Research Limited AucklandNew Zealand

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 *** evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still ***,we generated a chromosome-scale genome assembly of an autotetraploid male *** *** genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 *** 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 *** underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late *** genomics studies using paleoclimate data enabled us to discern the evolution of the species’adaptation to different historical *** 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 *** chromosome-level assembly of the autotetraploid *** genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of ***.

关键词： kiwiberry dioecism adaptive evolution paleoclimate GEA rapid softening

Genomics and morphometrics reveal the adaptive evolution of pikas

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Zoological Research 2022年第5期43卷 813-826页

作者： Rui-Xiang Tang Jiao Wang Yi-Fei Li Cheng-Ran Zhou Guan-Liang Meng Feng-Jun Li Yue Lan Megan Price Lars Podsiadlowski Yan Yu Xu-Ming Wang Yin-Xun Liu Bi-Song Yue Shan-Lin Liu Zhen-Xin Fan Shao-Ying Liu Key Laboratory of Bioresources and Ecoenvironment(Ministry of Education) College of Life SciencesSichuan UniversityChengduSichuan 610065China Sichuan Academy of Forestry ChengduSichuan 610081China Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE Department of PediatricsWest China Second University HospitalSichuan UniversityChengduSichuan 610041China BGI-Shenzhen ShenzhenGuangdong 518083China Zoological Research Museum Alexander Koenig Bonn D-53113Germany Department of Entomology China Agriculture UniversityBeijing 100193China Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life SciencesSichuan UniversityChengduSichuan 610065China

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 *** 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 ***, 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.

关键词： Pikas Genomics Morphometrics adaptive evolution Sensory and energy functions

Molecular mechanisms of adaptive evolution in wild animals and plants

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Science China(Life Sciences) 2023年第3期66卷 453-495页

作者： Yibo Hu Xiaoping Wang Yongchao Xu Hui Yang Zeyu Tong Ran Tian Shaohua Xu Li Yu Yalong Guo Peng Shi Shuangquan Huang Guang Yang Suhua Shi Fuwen Wei CAS Key Lab of Animal Ecology and Conservation Biology Chinese Academy of SciencesBeijing 100101China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunming 650091China State Key Laboratory of Systematic and evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key Laboratory of Genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650201China Institute of evolution and Ecology School of Life SciencesCentral China Normal UniversityWuhan 430079China College of Life Sciences Nanjing Normal UniversityNanjing 210023China State Key Laboratory of Biocontrol Guangdong Key Lab of Plant ResourcesSchool of Life SciencesSun Yat-sen University Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou 511458China

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and *** the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species *** 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 *** this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and ***,we focused on the adaptive evolution of morphological,behavioral,and physiological ***,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence ***,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and ***,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 ***,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

关键词： adaptive evolution adaptive trait coevolution comparative genomics convergent evolution genetic convergence molecular mechanism mutualism parasitism phenotype convergence