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gene duplication drove the loss of awn in sorghum.

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Molecular Plant 2021年第11期14卷 1831-1845页

作者： Leina Zhou Can Zhu Xiaojian Fang Hangqin Liu Shuyang Zhong Yan Li Jiacheng Liu Yang Song Xing Jian Zhongwei Lin National Maize Improvement Center Center for Crop Functional Genomics and Molecular BreedingJoint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationBeijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationChina Agricultural UniversityBeijing 100193China

Loss of the awn in some cereals including sorghum is a key transition during cereal domestication or improvement that has facilitated grain harvest and *** genetic basis for the loss of awn in sorghum during domestication or improvement remains ***,we identified a transcription factor gene awn1 encoding an ALOG domain,which is responsible for awn loss during sorghum domestication or ***1 arose from a gene duplication from chromosome 10 that translocated to chromosome 3,recruiting a new promoter from the neighbouring intergenic region filled with"noncoding DNA",and recreating the first exon and *** awn1 acquires high expr`ession after duplication and represses the elongation of awns in domesticated *** mapping revealed a high collinearity at awn1 paralog locus on chromosome 10 across cereals and awn growth and development was successfully reactivated on the rice spikelet by inactivating rice awn1 *** RNA-seq and DAP-seq revealed that as a transcription repressor,AWN1 directly bound to the motif in the regulatory regions from three MADS genes related to flower development and two genes DL and LKS2 for the development of awn,downregulated the expressions of these genes,and then repressed the elongation of *** preexistence of regulatory elements in the neighbouring intergenic region of awn1 before domestication signified that noncoding DNA may serve as a treasure trove for evolution during adaptation to a changing *** results supported that gene duplication can promptly drive the evolution of gene regulatory network.

关键词： DAP-seq awn gene duplication sorghum domestication and improvement

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

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Plant Communications 2023年第3期4卷 228-243页

作者： Hongyu Chen Miaoxian Guo Shuting Dong Xinling Wu Guobin Zhang Liu He Yuannian Jiao Shilin Chen Li Li Hongmei Luo Key Laboratory of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People’s Republic of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Shandong University of Traditional Chinese Medicine Jinan 250355China State Key Laboratory of Crop Biology Shandong Agricultural UniversityTaian 271018China College of Agronomy Shandong Agricultural UniversityTaian 271018China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of the Chinese Academy of Sciences Beijing 100049China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Chengdu University of Traditional Chinese Medicine Chengdu 611137China Robert W.Holley Center for Agriculture and Health USDA-ARSCornell UniversityIthacaNY 14853USA Plant Breeding and genetics Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA

Artemisia argyi Le´*** Vant.,a perennial Artemisia herb with an intense fragrance,is widely used in traditional medicine in China and many other Asian ***,we present a chromosome-scale genome assembly of *** comprising 3.89 Gb assembled into 17 *** and comparative genomic analyses revealed that *** underwent a recent lineage-specificwhole-genomeduplication(WGD)event after divergence fromArtemisia annua,resulting in two *** the diploid ancestral genome of ***,and unbiased subgenome evolution was *** recent WGD led to a large number of duplicated genes in the *** *** of the terpene synthase(TPS)gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in *** particular,we identified a typical germacrene D synthase gene cluster within the expanded TPS gene *** entire biosynthetic pathways of germacrenes,(+)-borneol,and(+)-camphor were elucidated in *** addition,partial deletion of the amorpha-4,11-diene synthase(ADS)gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in *** study provides newinsights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.

关键词： Artemisia argyi subgenome evolution gene duplication terpene synthase germacrene synthase nonartemisinin production

Allelic Polymorphism,gene duplication and Balancing Selection of MHC Class ⅡB genes in the Omei Treefrog(Rhacophorus omeimontis)

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Asian Herpetological Research 2016年第1期7卷 1-11页

作者： Li HUANG Mian ZHAO Zhenhua LUO Hua WU Institute of Evolution and Ecology International Research Centre of Ecology and EnvironmentSchool of Life SciencesCentral China Normal University

The worldwide declines in amphibian populations have largely been caused by infectious fungi and bacteria. Given that vertebrate immunity against these extracellular pathogens is primarily functioned by the major histocompatibility complex（MHC） class Ⅱ molecules, the characterization and the evolution of amphibian MHC class Ⅱ genes have attracted increasing attention. The polymorphism of MHC class Ⅱ genes was found to be correlated with susceptibility to fungal pathogens in many amphibian species, suggesting the importance of studies on MHC class Ⅱ genes for amphibians. However, such studies on MHC class Ⅱ gene evolution have rarely been conducted on amphibians in China. In this study, we chose Omei treefrog（Rhacophorus omeimontis）, which lived moist environments easy for breeding bacteria, to study the polymorphism of its MHC class Ⅱ genes and the underlying evolutionary mechanisms. We amplified the entire MHC class ⅡB exon 2 sequence in the R. omeimontis using newly designed primers. We detected 102 putative alleles in 146 individuals. The number of alleles per individual ranged from one to seven, indicating that there are at least four loci containing MHC class ⅡB genes in R. omeimontis. The allelic polymorphism estimated from the 102 alleles in R. omeimontis was not high compared to that estimated in other anuran species. No significant gene recombination was detected in the 102 MHC class ⅡB exon 2 sequences. In contrast, both gene duplication and balancing selection greatly contributed to the variability in MHC class ⅡB exon 2 sequences of R. omeimontis. This study lays the groundwork for the future researches to comprehensively analyze the evolution of amphibian MHC genes and to assess the role of MHC gene polymorphisms in resistance against extracellular pathogens for amphibians in China.

关键词： MHC class ⅡB polymorphism gene duplication balancing selection Rhacophorus omeimontis

维普期刊数据库

Higher tRNA gene duplication in mitogenomes of praying mantises(Dictyoptera,Mantodea) and the phylogeny within Mantodea

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Higher tRNA gene duplication in mitogenomes of praying manti...

The evolution and functional divergence of 10 Apolipoprotein D-like genes in Nilaparvata lugens

浙江省动物学会第十三次会员代表大会暨学术研讨会

作者： Zhang Le-Ping Yu Dan-Na Kenneth B.Storey Cheng Hong-Yi Zhang Jia-Yong College of Chemistry and Life Science Zhejiang Normal University Key lab of wildlife biotechnology conservation and utilization of Zhejiang Province Zhejiang Normal University Department of Biology Carleton University

We acquired 21 complete mitogenomes and 6 nearly complete mitogenomes of mantises belonging to 8 families(Hymenopodidae,Iridopterygidae,Mantidae,Metallyticidae,Sibyllidae,Tarachodidae,Thespidae,Toxoderidae)using 14 pairs of mantid specific primer sets and found that 5 species of mantises have duplicate copies(2-4)of trnR:Ambivia undata,Creobroter jiangxiensis,Creobroter urbanus,Phyllothelys *** Theopropus elegans while two novel gene arrangements CR-I-NCR-I-NCR-I-NCR-I-NCR-I-NCR*-Q-M and COII-K*-D*-K-D*-K-D*-K-D were found in Schizocephala bicornis and Stenotoxodera porioni,*** multiple copies of trnR are caused by independent *** gene arrangements in Stenotoxodera porioni with three identical copies of trnK can be explained as mid-way through the TDRL process while the form of gene arrangement in Schizocephala bicornis is *** the phylogeny at the family level,the monophyly of Liturgusidae and Iridopterygidae was supported,whereas the monophyly of Hymenopodidae,Mantidae and Tarachodidae wasn’*** features of mantis mitochondrial genomes including high duplication rates of trnR,trnK and trnl indicate that Mantodea mitochondrial genomes maybe a useful model system for studying gene ***,derived gene arrangements may not be appropriate for phylogenetic inference in Mantodea as they aren’t synapomorphy and aren’t shared by close relatives.

关键词： Mantodea mitochondrial genome gene duplication phylogeny

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Insect Science 2024年第1期31卷 91-105页

作者： Jia-Bao Lu Peng-Peng Ren Qiao Li Fang He Zhong-Tian Xu Sai-Nan Wang Jian-Ping Chen Jun-Min Li Chuan-Xi Zhang Citrus Research Institute Southwest University/Chinese Academy of Agricultural SciencesNational Engineering Research Center for CitrusChongqingChina Technology Center of Wuhan Customs District HubeiChina Institute of Insect Science Zhejiang UniversityHangzhouChina

Apolipoprotein D(ApoD),a member of the lipocalin superfamily of proteins,is involved in lipid transport and stress *** only a single copy of the ApoD gene is found in humans and some other vertebrates,there are typically several ApoD-like genes in *** date,there have been relatively few studies that have examined the evolution and functional differentiation of ApoD-like genes in insects,particularly hemi-metabolous *** this study,we identified 10 ApoD-like genes(NlApoD1−10)with distinct spatiotemporal expression patterns in Nilaparvata lugens(BPH),which is an important pest of ***1−10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2,NlApoD3−5,and NlApoD7/8,and show sequence and gene structural divergence in the coding regions,indicating that multiple gene duplication events occurred during *** analysis revealed that NlApoD1−10 can be clustered into 5 clades,with NlApoD3−5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae *** screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival,whereas NlApoD4/5 are highly expressed in testes,and might play roles in ***,stress response analysis revealed that NlApoD3−5/9,NlApoD3−5,and NlApoD9 were up-regulated after treatment with lipopolysaccharide,H2O2,and ultraviolet-C,respectively,indicating their potential roles in stress resistance.

关键词： Apolipoprotein D BPH evolution functional divergence gene duplication NIApoD

Duplicated chalcone synthase(CHS)genes modulate flavonoid production in tea plants in response to light stress

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Journal of Integrative Agriculture 2024年第6期23卷 1940-1955页

作者： Mingzhuo Li Wenzhao Wang Yeru Wang Lili Guo Yajun Liu Xiaolan Jiang Liping Gao Tao Xia State Key Laboratory of Tea Plant Biochemistry and Utilization Anhui Agricultural UniversityHefei 230036China School of Life Sciences Anhui Agricultural UniversityHefei 230036China College of Horticulture Northwest A&F UniversityYangling 712100China Department of Plant and Microbial Biology North Carolina State UniversityRaleigh 27606NCUSA

In tea plants,the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor *** the downstream mechanisms of flavonoid biosynthesis have been extensively studied,the role of chalcone synthase(CHS)in this secondary metabolic process in tea plants remains less *** this study,we compared the evolutionary profile of the flavonoid metabolism pathway and discovered that gene duplication of CHS occurred in tea *** identified three CsCHS genes,along with a CsCHS-like gene,as potential candidates for further functional *** the CsCHS-like gene,the CsCHS genes effectively restored flavonoid production in Arabidopsis ***,CsCHS transgenic tobacco plants exhibited higher flavonoid compound accumulation compared to their wild-type *** notably,our examination of promoter and gene expression levels for the selected CHS genes revealed distinct responses to UV-B stress in tea *** findings suggest that environmental factors such as UV-B exposure could have been the key drivers behind the gene duplication events in CHS.

关键词： tea flavonoids biosynthesis CHS gene duplication UV-B stress

维普期刊数据库

duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

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Cell Research 2006年第5期16卷 507-518页

作者： Danhua Jiang~(1,2) Changsong Yin~1 Aiping Yu~(1,3) Xiaofan Zhou~1 Wanqi Liang~(1,4) Zheng Yuan~1 Yun Xu~1 Qingbo Yu~1 Tieqiao Wen~2 Dabing Zhang~(1,4) ~1SJTU-SIBS-PSU Joint Center for Life Sciences,School of Life Science and Biotechnology,Shanghai Jiao Tong University 800 Dongchuan Road,Shanghai 200240, China ~2School of Life Science,Shanghai University,99 Shangda Road,Shanghai 200444,China ~3College of Life and Environment Sciences,Shanghai Normal University,100 Guilin Road, Shanghai 200234,China ~4Key Laboratory of Agricultural genetics and Breeding,Agro-biotech Research Center,Shanghai Academy of Agricultural Sciences,2901 Beidi Road,Shanghai 201106,China SJTU-SIBS-PSUJointCenterforLifeSciences SchoolofLifeScienceandBiotechnologyShanghaiJiaoTongUniversity800DongchuanRoadShanghai200240China SchoolofLifeScience ShanghaiUniversity99ShangdaRoadShanghai200444

To understand the expansion of multicopy microRNA (miRNA) families in plants,we localized the reported miRNAgenes from Arabidopsis and rice to their chromosomes,respectively,and observed that 37% of 117 miRNA genes fromArabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the *** order to characterizewhether the expression diversification has occurred among plant multicopy miRNA family members,we designed PCRprimers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and *** from RT-PCR datasuggest that the transcribed precursors of members within the same miRNA family were present at different *** addition,although miR160 and miR162 sequences were conserved in Arabidopsis and rice,we found that theexpression patterns of these genes differed between the two *** data suggested that expression diversifica-tion has occurred in multicopy miRNA families,increasing our understanding of the expression regulation of miRNAsin plants.

关键词： gene duplication microRNA multicopy

A recent burst of gene duplications in Triticeae

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Plant Communications 2022年第2期3卷 1-12页

作者： Xiaoliang Wang Xueqing Yan Yiheng Hu Liuyu Qin Daowen Wang Jizeng Jia Yuannian Jiao State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China College of Agronomy Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouHenan 450046China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

gene duplication provides raw genetic materials for evolution and potentially novel genes for crop *** two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been ***,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae *** investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the *** also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of *** subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread ***,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of *** results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.

关键词： gene duplication transposable elements gene dosage hexaploid wheat Triticeae agronomic traits

Genome-wide identification and comparative analysis of lipocalin families in Lepidoptera with an emphasis on Bombyx mori

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Insect Science 2023年第1期30卷 15-30页

作者： Yan-Yan Zhou Yue Jin Shuai-Qi Liu Shi-Liang Xu Yu-Xin Huang Yu-Song Xu Lian-Gen Shi Hua-Bing Wang Department of Economic Zoology College of Animal SciencesZhejiang UniversityHangzhouChina

Lipocalins exhibit functional diversity,including roles in retinol transport,invertebrate cryptic coloration,and stress ***,genome-wide identification and characterization of lipocalin in the insect lineage have not been thoroughly ***,we found that a lineage-specific expansion of the lipocalin genes in Lepidoptera occurred in large part due to tandem duplication events and several lipocalin genes involving insect coloration were expanded more via tandem duplication in butterflies.A comparative analysis of conserved motifs showed both conservation and divergence of lepidopteran lipocalin family protein structures during *** observe dynamic changes in tissue expression preference of paralogs in Bombyx mori,suggesting differential contribution of paralogs to specific organ functions during *** localization experiments revealed that lipocalins localize to the cytoplasm,nuclear membrane,or nucleus in BmN ***,several lipocalin genes exhibited divergent responses to abiotic and biotic stresses,and 1 lipocalin gene was upregulated by 30o fold in *** results suggest that lipocalins act as signaling components in defense responses by mediating crosstalk between abiotic and biotic stress *** study deepens our understanding of the comprehensive characteristics of lipocalins in insects.

关键词： functional divergence gene duplication Lepidoptera lipocalin