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

In tea plants,the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor profile.While 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 clear.In this study,we compared the evolutionary profile of the flavonoid metabolism pathway and discovered that gene duplication of CHS occurred in tea plants.We identified three CsCHS genes,along with a CsCHS-like gene,as potential candidates for further functional investigation.Unlike the CsCHS-like gene,the CsCHS genes effectively restored flavonoid production in Arabidopsis chs-mutants.Additionally,CsCHS transgenic tobacco plants exhibited higher flavonoid compound accumulation compared to their wild-type counterparts.Most notably,our examination of promoter and gene expression levels for the selected CHS genes revealed distinct responses to UV-B stress in tea plants.Our findings suggest that environmental factors such as UV-B exposure could have been the key drivers behind the gene duplication events in CHS.

Functional diversifications of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.

Different expression patterns of duplicated PHANTASTICA-like genes in Lotus japonicus suggest their divergent functions during compound leaf development

Recent studies on leaf development demonstrate that the mechanism on the adaxial-abaxial polarity pattern formation could be well conserved among the far-related species, in which PHANTASTICA （PAHN）-Iike genes play important roles. In this study, we explored the conservation and diversity on functions of PHAN-Iike genes during the compound leaf development in Lotusjaponicus, a papilionoid legume. Two PHAN-Iike genes in L. japonicus, LjPHANa and LjPHANb, were found to originate from a gene duplication event and displayed different expression patterns during compound leaf development. Two mutants, reduced leafletsl （rell） and reduced leaflets3 （rel3）, which exhibited decreased adaxial identity of leaflets and reduced leaflet initiation, were identified and investigated. The expression patterns of both LjPHANs in rel mutants were altered and correlated with abnormalities of compound leaves. Our data suggest that LjPHANa and LjPHANb play important but divergent roles in regulating adaxial-abaxial polarity of compound leaves in L. japonicus.

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

The evolution of the central nervous system（CNS） is one of the most striking changes during the transition from invertebrates to vertebrates. As a major source of genetic novelties,gene duplication might play an important role in the functional innovation of vertebrate CNS.In this study,we focused on a group of CNS-biased genes that duplicated during early vertebrate evolution.We investigated the tempo-spatial expression patterns of 33 duplicate gene families and their orthologs during the embryonic development of the vertebrate Xenopus laevis and the cephalochordate Brachiostoma belcheri.Almost all the identified duplicate genes are differentially expressed in the CNS in Xenopus embryos,and more than 50%and 30%duplicate genes are expressed in the telencephalon and mid-hindbrain boundary,respectively,which are mostly considered as two innovations in the vertebrate CNS.Interestingly,more than 50%of the amphioxus orthologs do not show apparent expression in the CNS in amphioxus embryos as detected by in situ hybridization,indicating that some of the vertebrate CNS-biased duplicate genes might arise from non-CNS genes in invertebrates.Our data accentuate the functional contribution of gene duplication in the CNS evolution of vertebrate and uncover an invertebrate non-CNS history for some vertebrate CNS-biased duplicate genes.

Faster evolution of Z-linked duplicate genes in chicken

It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females （females have ZW sex chromosome）. We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.

On the origin and evolution of new genes——a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.

Genome-wide identification and co-expression network analysis of the Os NF-Y gene family in rice

Nuclear factor Y(NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 Os NF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of Os NF-Y differentially accumulated in a tissue-specific,preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the Os NF-Y gene family.Nine Os NF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that Os NF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development.Co-expression analysis also revealed that Os NF-Y genes might interact with each other,suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.

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

To understand the expansion ofmulticopy microRNA （miRNA） families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miRl60 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Molecular evolution of the rice miR395 gene family

MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.

Comprehensive identification and analyses of the Hsf gene family in the whole-genome of three Apiaceae species

Apiaceae is a major family from Apiales and includes many important vegetable and medicinal crops.Heat shock transcription factors(Hsf)play important roles in heat tolerance during plant development.Here,we conducted systematic analyses of the Hsf gene family in three Apiaceae species,including 17 Apium graveolens(celery),32 Coriandrum sativum(coriander),and 14 Daucus carota(carrot).A total of 73 Hsf genes were identified in three representative species,including Arabidopsis thaliana,Vitis vinifera,and Lactuca sativa.Whole-genome duplication played important roles in the Hsf gene family’s expansion within Apiaceae.Interestingly,we found that coriander had more Hsf genes than celery and carrot due to greater expansion and fewer losses.Twenty-seven branches of the phylogenetic tree underwent considerable positive selection in these Apiaceae species.We also explored the expression patterns of Hsf genes in three plant organs.Collectively,this study will serve as a rich gene resource for exploring the molecular mechanisms of heat tolerance.Additionally,this is the first study to report on the Hsf gene family in Apiaceae;thus,our research will provide guidance for future comparative and functional genomic studies on the Hsf gene family and others in Apiaceae.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development,and phytohormone and abiotic stress responses

Background： RING H2 finger E3 ligase （RH2FE3） genes encode cysteine rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported. Methods： We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated KJKs values of G hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all versus all BLASTP searches. We predicted cis regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction （qRT PCR） analysis. Results： We investigated 140 G hirsutum, 80 G. orboreum, and evolutionary mechanisms and compared them with orthologs 89 G. roimondii putative RH2FB genes and their in Arobidopsis and rice. A domain based analysis of the G hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G hirsutum chromosomes, and 60 duplication events （4 tandem and 56 segmental duplications） and 98 orthologs were detected, cis elements were detected in the promoter regions of G hirsutum RH2FE3 genes. Microarray data and qRT PCR analyses showed that G hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the （brassinolide, gibberellic acid （GA）, indole 3-acetic acid drought, and salt）. dentified genes were up regulated in response to phytohormones （IAA）, and salicylic acid （SA）） and abiotic stresses （cold, heat, Conclusions： The genome wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis element prediction, and expression profile analysis of G hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G hirsutum RH2FE3 genes.

Allelic Polymorphism,Gene Duplication and Balancing Selection of MHC Class ⅡB Genes in the Omei Treefrog(Rhacophorus omeimontis)

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.

Evolutionary Mode of Metallothioneins Inferred from Cd-MT Genes of Tetrahymena

From Tetrahymena thermophila （strain BF5）, the coding region of Cd-MT gene was cloned and sequenced. and identified as MTT1 isoform. A serial duplicate structure is discovered in its amino acid sequence, which separates the coding region into three parts （Part 1：7-61; Part 2：64-118; Part 3：122-162）. The alignments among them and comparison with the corresponding parts of MT1 isoform suggest that MT1 and MTT1 isoforms both come from the same ancient gene that is homologous to Part 1, and Cd-MTs of Tetrahymena are aroused by such ancient gene duplication. The prediction of secondary structures and the analysis of the disulfide-bonding state of cysteine show that there are a lot of differences between MT1 and MTT1 isoforms, which maybe relate to their function mechanism.

Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Electrophoretic Analysis of Isozymes and Discussion about Species Differentiation in Three Species of Genus Gymnocypris

By using the method of electrophoresis,three isozymes (lactate dehydrogenase,malate dehydrogenase and esterase) of three species of genus Gymnocypris were described and analyzed from North Tibet in this paper. The results showed that all three isozymes presented interspecific difference and distinct differentiation among individuals in the same population,and there was no electrophorectic difference between males and females. Analysis of relationships among three naked carps indicated a high degree of similarity between G. selincuoensis and G. cuoensis ,whereas low degree between G. selincuoensis and G. namensis . Furthermore,three isozymes presented expression of null alleles,and the duplicate genes of LDH A 2,LDH B 2,s MDH A 2 and m MDH B 2 also expressed in some individuals. Compared to other tetraploid fishes,three naked carps retained more functional duplicate genes and null alleles. This suggests fishes of genus Gymnocypris are at the early stage of evolution after polyploidization than that of fishes of Catostomidae,it directly related to the later time of schizothoracine fishes originate as well as severe environment.

Comparative analysis of SIMILAR to RCD ONE(SRO)family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development

Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so far.Results A total of 36 SRO genes were identified from four cotton species.Phylogenetic analysis divided these genes into three groups with distinct structure.Syntenic and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,respectively.Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes.In promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and development.Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes.Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues.In addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental processes.Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.

Inheritance of Ear Tip-Barrenness Trait in Maize

The aim of this paper is to study the inheritance pattern of ear tip-barrenness trait in maize （Zea mays L.）. Ear tipbarrenness trait in maize can be classified into two types, tip-barren and tip-barrenless. Two inbred lines, lx01-3 （tipbarrenless type）, wx04-1 （tip-barren type）, and their F1, F2, BC1, BC2 generations were analyzed on their ear tip-barrenness types. Results showed that F1 was tip-barren type; the ratio of tip-barren type versus tip-barrenless type followed a 12.78： 1 ratio in F2 segregation population and a 2.75：1 ratio in BC1. Z2 test indicated that the trait of ear tip-barrenness type followed an inheritance pattern of 2 duplicate dominant genes. SPSS analysis indicated that the trait of ear tip-barrenness length is of abnormal distribution. Above results mean that： （1） The trait of maize ear tip-barrenness type is controlled by 2 duplicate dominant genes; tip-barren type is dominant over tip-barrenless type; （2） the trait of tip-barrenness length is a quantitative character controlled by polygene with major genes expected.

Science Letters:Two ancient rounds of polyploidy in rice genome

An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.

The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization

Since the discovery of the first transposon by Dr.Barbara McClintock,the prevalence and diversity of transposable elements(TEs)have been gradually recognized.As fundamental genetic components,TEs drive organismal evolution not only by contributing functional sequences(e.g.,regulatory elements or“controllers”as phrased by Dr.McClintock)but also by shuffling genomic sequences.In the latter respect,TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest.In response to the development of this field,we herein attempt to provide an overview of TEmediated duplication by focusing on common rules emerging across duplications generated by different TE types.Specifically,despite the huge divergence of transposition machinery across TEs,we identify three common features of various TE-mediated duplication mechanisms,including end bypass,template switching,and recurrent transposition.These three features lead to one common functional outcome,namely,TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization.Therefore,the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates.We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

Targeted Mutagenesis of Duplicated Genes in Caenorhabditis elegans Using CRISPR-Cas9

CRISPR （clustered regularly interspaced short palindromic repeats）-Cas9-based genome editing has revolutionized func- tional genomics in many biological research fields. The specificity and potency of CR1SPR-Cas9 genome editing make it ideal for investigating the function of genes in vivo （Hsu et al., 2014）. Gene duplication is a key driver of evolu- tionary novelty （Taylor and Raes, 2004）. However, duplicated genes with near-identical sequences and functional redun- dancy have posed challenges for genetic analysis （Woollard, 2005）. The functions of duplicated genes can be assessed by simultaneous knockdown using homology-based methods such as RNA interference （RNAi） （Tischler et al., 2006）, Generation of double or triple mutants is an alternative way to assess functional redundancy of duplicated genes, However, generation of such compound mutants by forward or reverse genetic methods is time consuming.