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| 1 | Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms显示文摘Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (~120 million years ago [Ma], ~66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms. | Shengdan Wu Baocai Han Yuannian Jiao | 2020 | Molecular Plant2020，13，1： | 21 |
| 2 | A Transcriptional Network Promotes Anthocyanin Biosynthesis in Tomato Flesh显示文摘Dietary anthocyanins are important health-promoting antioxidants that make a major contribution to the quality of fruits. It is intriguing that most tomato cultivars do not produce anthocyanins in fruit. However, the purple tomato variety Indigo Rose, which has the dominant Aft locus combined with the recessive atv locus from wild tomato species, exhibits light-dependent anthocyanin accumulation in the fruit skin. Here, we report that Aft encodes a functional anthocyanin activator named SlAN2-like, while atv encodes a nonfunctional version of the anthocyanin repressor SlMYBATV. The expression of SlAN2-like is responsive to light, and the functional SlAN2-like can activate the expression of both anthocyanin biosynthetic genes and their regulatory genes, suggesting that SlAN2-like acts as a master regulator in the activation of anthocyanin biosynthesis. We further showed that cultivated tomatoes contain nonfunctional alleles of SlAN2-like and therefore fail to produce anthocyanins. Consistently, expression of a functional SlAN2-like gene driven by the fruit-specific promoter in a tomato cultivar led to the activation of the entire anthocyanin biosynthesis pathway and high-level accumulation of anthocyanins in both the peel and flesh. Taken together, our study exemplifies that efficient engineering of complex metabolic pathways could be achieved through tissue-specific expression of master transcriptional regulators. | Chuanlong Sun Lei Deng Minmin Du Jiuhai Zhao Qian Chen Tingting Huang Hongling Jiang Chang-Bao Li Chuanyou Li | 2020 | Molecular Plant2020，13，1： | 17 |
| 3 | Diversity and evolution of MicroRNA gene clusters显示文摘microRNA(miRNA) gene clusters are a group of miRNA genes clustered within a proximal distance on a chromosome.Although a large number of miRNA clusters have been uncovered in animal and plant genomes,the functional consequences of this arrangement are still poorly understood.Located in a polycistron,the coexpressed miRNA clusters are pivotal in coordinately regulating multiple processes,including embryonic development,cell cycles and cell differentiation.In this review,based on recent progress,we discuss the genomic diversity of miRNA gene clusters,the coordination of expression and function of the clustered miRNAs,and the evolutionarily adaptive processes with gain and loss of the clustering miRNA genes mediated by duplication and transposition events. | ZHANG YanFeng,ZHANG Rui & SU Bing State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China | 2009 | Science China(Life Sciences)2009，52，3： | 7 |
| 4 | Antibiotic Treatment Drives the Diversification of the Human Gut Resistome显示文摘Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that shortterm antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ~3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota. | Jun Li Elizabeth A.Rettedal Eric van der Helm Mostafa Ellabaan Gianni Panagiotou Morten O.A.Sommer | 2019 | Genomics, Proteomics & Bioinformatics2019，17，1： | 4 |
| 5 | Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors显示文摘We analyze the global structure and evolution of human gene coexpression networks driven by new gene integration. When the Pearson correlation coefficient is greater than or equal to 0.5, we find that the coexpression network consists of 334 small components and one 'giant' connected subnet comprising of 6317 interacting genes. This network shows the properties of power-law degree distribution and small-world. The average clustering coefficient of younger genes is larger than that of the elderly genes(0.6685 vs. 0.5762). Particularly, we find that the younger genes with a larger degree also show a property of hierarchical architecture. The younger genes play an important role in the overall pivotability of the network and this network contains few redundant duplicate genes. Moreover, we find that gene duplication and orphan genes are two dominant evolutionary forces in shaping this network. Both the duplicate genes and orphan genes develop new links through a 'rich-gets-richer'mechanism. With the gradual integration of new genes into the ancestral network, most of the topological structure features of the network would gradually increase. However, the exponent of degree distribution and modularity coefficient of the whole network do not change significantly, which implies that the evolution of coexpression networks maintains the hierarchical and modular structures in human ancestors. | Jian Zu Yuexi Gu Yu Li Chentong Li Wenyu Zhang Yong E.Zhang UnJin Lee Li Zhang Manyuan Long | 2019 | Science China(Life Sciences)2019，62，4： | 3 |
| 6 | Transposable elements significantly contributed to the core promoters in the human genome显示文摘Transposable elements(TEs) are major components of the human genome constituting at least half of it. More than half a century ago, Barbara McClintock and later Roy Britten and Eric Davidson have postulated that they might be major players in the host gene regulation. We have scanned a large amount of data produced by ENCODE project for active transcription binding sites(TFBSs) located in TE-originated parts of polymerase II promoters. In total, more than 35,000 promoters in six different tissues were analyzed and over 26,000 of them harbored TEs. Moreover, these TEs usually provide one or more of TFBSs in the host promoters, which resulted in more than 6% of active TFBSs in these regions located in the TE-originated sequences. Rewiring of transcription circuits played a major role in mammalian evolution and consequently increased their functional and morphological diversity. In this large-scale analysis, we have demonstrated that TEs contributed a large fraction of human TFBSs. Interestingly,these TFBSs usually act in a tissue-specific manner. Thus, our study clearly showed that TEs played a significant role in shaping expression pattern in mammals and humans in particular. Furthermore, since several TE families are still active in our genome,they continue to influence not only our genome architecture but also gene functioning in a broader sense. | Marten Kellner Wojciech Maka?owski | 2019 | Science China(Life Sciences)2019，62，4： | 2 |
| 7 | Genomic data reveal high conservation but divergent evolutionary pattern of Polycomb/Trithorax group genes in arthropods显示文摘Eplgenetlc gene control is maintained by chromatln-assoclated Polycomb group (PcG)and Trithorax group (TrxG)genes,which act antagonistically via the interplay between PcG and TrxG regulation to generate silenced or permissive transcriptional states. In this study,we searched for PcG/TrxG genes in 180 arthropod genomes,covering all the sequenced arthropod genomes at the time of conducting this study,to perform a global investigation of PcG/TrxG genes in a phylogenetic frame.Results of ancestral state reconstruction analysis revealed that the ancestor of arthropod species has an almost complete repertoire of PcG/TrxG genes,and most of these genes were seldom lost above order level. The domain diversity analysis indicated that the PcG/TrxG genes show variable extent of domain structure changes;some of these changes could be associated with lineage-specific events.The likelihood ratio tests for selection pressure detected a number of PcG/TrxG genes which underwent episodic positive selection on the branch leading to the insects with holometabolous development.These results suggest that,despite their high conservation across arthropod species,different members of PcG/TrxG genes showed considerable differences in domain structure and sequence divergence in arthropod evolution.Our cross species comparisons using large-scale genomic data provide insights into divergent evolutionary pattern on highly conserved genes in arthropods. | Feng Jiang Qing Liu Xiang Liu Xian-Hui Wang Le Kang | 2019 | Insect Science2019，26，1： | 1 |
| 8 | Duplication and diversification of insulin genes in ray-finned fish显示文摘Insulin is a key hormone for the regulation of metabolism in vertebrates.Insulin is produced by pancreatic islet cells in response to elevated glucose levels and leads to the uptake of glucose by tissues such as liver and adipose tissue to store energy.Insulin also has additional functions in regulating development.Previous work has shown that the proglucagon gene,which encodes hormones counter regulating insulin,is duplicated in teleost fish,and that the peptide hormones encoded by these genes have diversified in function.I sought to determine whether similar processes have occurred to insulin genes in these species.Searches of fish genomes revealed an unexpected diversity of insulin genes.A triplication of the insulin gene occurred at the origin of teleost fish,however one of these three genes,insc,has been lost in most teleost fish lineages.The two other insulin genes,insa and insb,have been retained but show differing levels of selective constraint suggesting that they might have diversified in function.Intriguingly,a duplicate copy of the insa gene,which I named insab,is found in many fish.The coding sequenee encoded by insab genes is under weak selective constraint,with its predicted protein sequences losing their potential to be processed into a two-peptide hormone.However,these sequences have retained perfectly conserved cystine residues,suggesting that they maintain insulin's three-dimensional structure and therefore might modulate the processing and secretion of insulin produced by the other genes. | David M.Irwin | 2019 | Zoological Research2019，40，3： | 1 |
| 9 | A Single JAZ Repressor Controls the Jasmonate Pathway in Marchantia polymorpha显示文摘JAZ proteins are negative regulators of jasm onate responses,acting both as repressors of transcription factors and as co-receptors of JA-lle. The high redundancy of JAZ genes in angiosperms has hindered the characterization of a complete depletion of JAZ function. Moreover, the recent discovery that dn- OPDA is the jasmonate ligand in Marchantia polymorpha demonstrates that JA-lle is not the sole COI1/ JAZ ligand in land plants and highlights the importance of studying JAZ co-receptors in bryophytes? Here, we have exploited the low gene redundancy of the liverwort M. polymorpha to characterize the single MpJ4Z in this early diverging plant lineage. We clarify the phylogenetic history of the TIFY family, demonstrate that MpJAZ is the ortholog of AtJAZ with a conserved function, and characterize its repressor activity of dn-OPDA resp on ses. Our results show that, con sistent with previous findings in Arabidopsis, MpJAZ represses jasmonates biosynthesis, senescence, and plant defenses, and promotes cell growth and reproductive fitness, highlighting the power of studies in Marchantia. | Isabel Monte Jose M. Franco-Zorrilla Gloria Garcia-Casado Angel M. Zamarreno Jose M. Garcia-Mina Ryuichi Nishihama Takayuki Kohchi Roberto Solano | 2019 | Molecular Plant2019，12，2： | 1 |
| 10 | The correlation between clonal evolution and recurrent acute leukemia:A report of 2 cases显示文摘We report two cases of acute leukemia relapse resulting from clonal evolution in the course of disease. The case 1 was a 22-year-old female of acute non-lymphoblastic leukemia (ANLL)-M1, whose immunophenotypic and gene markers of leukemia cells had changed as compared with those at admission 10months ago, which indicates the evolution of leukemic clone. The case 2 was a 36-year -old female with acute lymphoblastic leukemia (ALL)-L2. Difference in the gene markers of leukemic clone were found between the three times of relapse. It was indicated the patient’S leukemia clone also had evolution in the course of disease. Clonal evolution may be caused by subclonal increase. The major clones were inhibited after induction therapy, but drug-resistant subclonal evaluation from some primary main clone could exist continuously and might proliferate further, which could result in leukemia relapse with change of immunophenotype and/or genotype. Clonal evolution might play an important role in the pathogenesis of some tumors in blood system. | 徐兵 周淑芸 | 1998 | Journal of Medical Colleges of PLA(China)1998，13，4： | 0 |
| 11 | Spatiotemporal expression of Pax genes in amphioxus: Insights into Pax-related organogenesis and evolution显示文摘The expression of four AmphiPax genes in 16 developmental stages and different organs in amphioxus (Branchiostoma belcheri) was investigated, finding those genes expressed throughout amphioxus life with temporal-specific (especially during embryogenesis and metamorphosis) and spatial-specific patterns. This study suggests that duplicated Pax genes in vertebrates might maintain most of their ancestral functions and also expand their expression patterns after the divergence of protochordates and vertebrates. | CHEN Lu1, ZHANG QiuJing1,2, WANG Wei1 & WANG YiQuan1 1Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China 2College of Life Sciences, Fujian Normal University, Fuzhou 350108, China | 2010 | Science China(Life Sciences)2010，53，8： | 0 |
| 12 | Markov Model Applied to Gene Evolution显示文摘The study of nucleotide substitution is very important both to our understanding of gene evolution and to reliable estimation of phylogenetic relationships. In this paper nucleotide substitution is assumed to be random and the Markov model is applied to the study of the evolution of genes. Then a non linear optimization approach is proposed for estimating substitution in real sequences. This substitution is called the 'Nucleotide State Transfer Matrix'. One of the most important conclusions from this work is that gene sequence evolution conforms to the Markov process. Also, some theoretical evidences for random evolution are given from energy analysis of DNA replication. | 季星来 孙之荣 | 2001 | Tsinghua Science and Technology2001，6，5： | 0 |
| 13 | Rediscovery and analysis of Phytophthora carbohydrate esterase(CE) genes revealing their evolutionary diversity显示文摘A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs. | QIAN Kun LI Deng-hui LIN Run-mao SHI Qian-qian MAO Zhen-chuan YANG Yu-hong FENG Dong-xin XIE Bing-yan | 2018 | Journal of Integrative Agriculture2018，17，4： | 0 |
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