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1.
Cytogenet Genome Res ; 159(1): 12-18, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31593956

RESUMO

The human genome harbors many duplicated segments, which sometimes show very high sequence identity. This may complicate assignment during genome assembly. One such example is in Xq28, where the arrangement of 2 recently duplicated segments varies between genome assembly versions. The duplicated segments comprise highly similar genes, including MAGEA3 and MAGEA6, which display specific expression in testicular germline cells, and also become aberrantly activated in a variety of tumors. Recently, a new gene was identified, CT-GABRA3, the transcription of which initiates inside the segmental duplication but extends far outside. According to the latest genome annotation, CT- GABRA3 starts near MAGEA3, with which it shares a bidirectional promoter. In an earlier annotation, however, the duplicated segment was positioned in the opposite orientation, and CT-GABRA3 was instead coupled with MAGEA6. To resolve this discrepancy, and based on the contention that genes connected by a bidirectional promoter are almost always co-expressed, we decided to compare the expression profiles of CT-GABRA3, MAGEA3, and MAGEA6. We found that in tumor tissues and cell lines of different origins, the expression of CT-GABRA3 was better correlated with that of MAGEA6. Moreover, in a cellular model of experimental induction with a DNA demethylation agent, activation CT-GABRA3 was associated with that of MAGEA6, but not with that of MAGEA3. Together these results support a connection between CT-GABRA3 and MAGEA6 and illustrate how promoter-sharing genes can be exploited to resolve genome assembly uncertainties.


Assuntos
Antígenos de Neoplasias/genética , Cromossomos Humanos X/genética , Proteínas de Neoplasias/genética , Regiões Promotoras Genéticas/genética , Receptores de GABA-A/genética , Duplicações Segmentares Genômicas/genética , Antígenos de Neoplasias/metabolismo , Epigênese Genética/genética , Duplicação Gênica/genética , Regulação Neoplásica da Expressão Gênica/genética , Genoma Humano/genética , Humanos , Proteínas de Neoplasias/metabolismo , Neoplasias/genética , Neoplasias/patologia , Células Tumorais Cultivadas
2.
Cytogenet Genome Res ; 159(2): 66-73, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31639787

RESUMO

The genomic region at 15q11.2q13 represents a hotspot for copy-number variations (CNVs) due to nonallelic homologous recombination. Previous studies have suggested that the development of 15q11.2q13 deletions in sperm may be affected by seasonal factors because patients with Prader-Willi syndrome resulting from 15q11.2q13 deletions on paternally derived chromosomes showed autumn-dominant birth seasonality. The present study aimed to determine the frequency of 15q11.2q13 CNVs in sperm of healthy men and clarify the effects of various environmental factors, i.e., age, smoking status, alcohol intake, and season, on the frequency. Thirty volunteers were asked to provide semen samples and clinical information once in each season of a year. The rates of 15q11.2q13 CNVs were examined using 2-color FISH. The results were statistically analyzed using a generalized estimating equation with negative binomial distribution and a log link function. Consequently, informative data were obtained from 83 samples of 26 individuals. The rates of deletions and duplications ranged from 0.04 to 0.48% and from 0.08 to 0.30%, respectively. The rates were not correlated with the age, smoking status, or alcohol intake. Sperm produced in winter showed 1.2 to 1.4-fold high rates for both deletions and duplications as compared with sperm produced in the other seasons; however, there was no significant difference. These results demonstrate high and variable CNV rates at 15q11.2q13 in sperm of healthy men. These CNVs appear to occur independent of the age, smoking status, or alcohol intake, while the effect of season remains inconclusive. Our results merit further validation.


Assuntos
Cromossomos Humanos Par 15/genética , Variações do Número de Cópias de DNA/genética , Espermatozoides/fisiologia , Adulto , Deleção Cromossômica , Duplicação Gênica/genética , Humanos , Masculino , Pessoa de Meia-Idade , Síndrome de Prader-Willi/genética , Adulto Jovem
3.
Genes (Basel) ; 10(9)2019 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-31480756

RESUMO

Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.


Assuntos
Arabidopsis/genética , Técnicas de Cultura de Células/métodos , Variações do Número de Cópias de DNA , Genoma de Planta , Técnicas de Cultura de Células/normas , Células Cultivadas , Duplicação Gênica , Frequência do Gene , Hipocótilo/citologia , Hipocótilo/genética , Transcriptoma
4.
Nat Commun ; 10(1): 4126, 2019 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-31511504

RESUMO

Interspecies hybrids often show some advantages over parents but also frequently suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out genetic incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in species such as fungi that can also propagate asexually. Here, to test this, we evolve in parallel and under relaxed selection more than 600 diploid yeast inter-specific hybrids that span from 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occur in both hybrids between young and well-established species. Our results show that the instability of ploidy in hybrid is an accessible path to spontaneous fertility recovery.


Assuntos
Fertilidade/genética , Duplicação Gênica , Genoma , Hibridização Genética , Poliploidia , Especificidade da Espécie , Fatores de Tempo , Leveduras/genética
5.
Genes (Basel) ; 10(9)2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31491991

RESUMO

Sex-determining genes have been successively isolated in several teleosts. In Odontesthes hatcheri and O. bonariensis, the amhy gene has been identified as a master sex-determining gene. However, whether this gene is conserved along related species is still unknown. In this study, the presence of amhy and its association with phenotypic sex was analyzed in 10 species of Odontesthes genus. The primer sets from O. hatcheri that amplify both amhs successfully generated fragments that correspond to amha and amhy in all species. The full sequences of amhy and amha isolated for four key species revealed higher identity values among presumptive amhy, including the 0.5 Kbp insertion in the third intron and amhy-specific insertions/deletions. Amha was present in all specimens, regardless of species and sex, whereas amhy was amplified in most but not all phenotypic males. Complete association between amhy-homologue with maleness was found in O. argentinensis, O. incisa, O. mauleanum, O. perugiae, O. piquava, O. regia, and O. smitti, whereas O. humensis, O. mirinensis, and O. nigricans showed varied degrees of phenotypic/genotypic sex mismatch. The conservation of amhy gene in Odontesthes provide an interesting framework to study the evolution and the ecological interactions of genotypic and environmental sex determination in this group.


Assuntos
Evolução Molecular , Peixes/genética , Duplicação Gênica , Processos de Determinação Sexual , Cromossomo Y/genética , Aclimatação , Animais , Sequência Conservada , Feminino , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Peixes/crescimento & desenvolvimento , Mutação INDEL , Masculino
6.
Genes (Basel) ; 10(9)2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31492001

RESUMO

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (VvGA2oxs, VvGA3oxs, and VvGA20oxs) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis GA2oxs, GA3oxs, and GA20oxs genes already reported, the VvGA2oxs, VvGA3oxs, and VvGA20oxs genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of VvGA2oxs, VvGA3oxs, and VvGA20oxs gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 GAoxs genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of VvGAox genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of VvGA2oxs and VvGA20oxs in different tissues at different developmental stages of grapes were relatively higher than that of VvGA3oxs. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the GAoxs gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some VvGA2oxs was upregulated under GA3 treatment. Simultaneously, some VvGA3oxs and VvGA20oxs were upregulated under uniconazole treatment. In a nutshell, the GA2ox gene mainly functions to inactivate biologically active GAs, while GA20ox mainly degrades C20 gibberellins, and GA3ox is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of VvGAoxs would provide a basis for understanding the evolution and function of the VvGAox gene family in a grape plant.


Assuntos
Giberelinas/metabolismo , Oxigenases de Função Mista/genética , Proteínas de Plantas/genética , Vitis/genética , Códon/genética , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Oxigenases de Função Mista/metabolismo , Proteínas de Plantas/metabolismo , Seleção Genética , Estresse Fisiológico , Regulação para Cima , Vitis/enzimologia
7.
BMC Bioinformatics ; 20(1): 460, 2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492104

RESUMO

BACKGROUND: Uncovering the evolutionary principles of gene coexpression network is important for our understanding of the network topological property of new genes. However, most existing evolutionary models only considered the evolution of duplication genes and only based on the degree of genes, ignoring the other key topological properties. The evolutionary mechanism by which how are new genes integrated into the ancestral networks are not yet to be comprehensively characterized. Herein, based on the human ribonucleic acid-sequencing (RNA-seq) data, we develop a new evolutionary model of gene coexpression network which considers the evolutionary process of both duplication genes and de novo genes. RESULTS: Based on the human RNA-seq data, we construct a gene coexpression network consisting of 8061 genes and 638624 links. We find that there are 1394 duplication genes and 126 de novo genes in the network. Then based on human gene age data, we reproduce the evolutionary process of this gene coexpression network and develop a new evolutionary model. We find that the generation rates of duplication genes and de novo genes are approximately 3.58/Myr (Myr=Million year) and 0.31/Myr, respectively. Based on the average degree and coreness of parent genes, we find that the gene duplication is a random process. Eventually duplication genes only inherit 12.89% connections from their parent genes and the retained connections have a smaller edge betweenness. Moreover, we find that both duplication genes and de novo genes prefer to develop new interactions with genes which have a large degree and a large coreness. Our proposed model can generate an evolutionary network when the number of newly added genes or the length of evolutionary time is known. CONCLUSIONS: Gene duplication and de novo genes are two dominant evolutionary forces in shaping the coexpression network. Both duplication genes and de novo genes develop new interactions through a "rich-gets-richer" mechanism in terms of degree and coreness. This mechanism leads to the scale-free property and hierarchical architecture of biomolecular network. The proposed model is able to construct a gene coexpression network with comprehensive biological characteristics.


Assuntos
Evolução Molecular , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Modelos Genéticos , Duplicação Gênica , Humanos , Análise de Sequência de RNA
8.
Nat Commun ; 10(1): 4237, 2019 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-31530873

RESUMO

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.


Assuntos
Cromossomos de Insetos/genética , Resistência a Inseticidas , Inseticidas/farmacologia , Mariposas/efeitos dos fármacos , Mariposas/genética , Animais , Duplicação Gênica , Genoma de Inseto , Proteínas de Insetos/genética , Proteínas de Insetos/metabolismo , Mariposas/metabolismo , Feromônios/metabolismo , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas , Receptores Odorantes/genética , Receptores Odorantes/metabolismo
9.
Genes (Basel) ; 10(9)2019 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-31500388

RESUMO

Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Polimorfismo Genético , Evolução Molecular , Conversão Gênica , Duplicação Gênica
10.
Nat Commun ; 10(1): 4023, 2019 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492844

RESUMO

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a global threat to wheat production. Aegilops tauschii, one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst-resistant allele YrAS2388R has duplicated 3' untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P. striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii-derived synthetic wheat; it is absent in 100% (n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species.


Assuntos
Regiões 3' não Traduzidas/genética , Resistência à Doença/genética , Genes de Plantas/genética , Hordeum/genética , Doenças das Plantas/genética , Triticum/genética , Alelos , Basidiomycota/fisiologia , Mapeamento Cromossômico , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Hordeum/classificação , Hordeum/microbiologia , Mutação , Filogenia , Doenças das Plantas/microbiologia , Plantas Geneticamente Modificadas , Triticum/classificação , Triticum/microbiologia
11.
Nat Commun ; 10(1): 3444, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31371717

RESUMO

Plants synthesize numerous ecologically specialized, lineage-specific metabolites through biosynthetic gene duplication and functional specialization. However, it remains unclear how duplicated genes are wired into existing regulatory networks. We show that the duplicated gene CYP82C2 has been recruited into the WRKY33 regulon and indole-3-carbonylnitrile (ICN) biosynthetic pathway through exaptation of a retroduplicated LINE retrotransposon (EPCOT3) into an enhancer. The stepwise development of a chromatin-accessible WRKY33-binding site on EPCOT3 has potentiated the regulatory neofunctionalization of CYP82C2 and the evolution of inducible defense metabolite 4-hydroxy-ICN in Arabidopsis thaliana. Although transposable elements (TEs) have long been recognized to have the potential to rewire regulatory networks, these results establish a more complete understanding of how duplicated genes and TEs contribute in concert to chemical diversity and pathogen defense.


Assuntos
Arabidopsis/genética , Elementos de DNA Transponíveis/genética , Regulação da Expressão Gênica de Plantas , Imunidade Vegetal/imunologia , Regulon/genética , Regulon/fisiologia , Arabidopsis/imunologia , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Sítios de Ligação , Vias Biossintéticas/genética , Sistema Enzimático do Citocromo P-450/genética , Evolução Molecular , Duplicação Gênica , Genoma de Planta , Glucosinolatos/metabolismo , Indóis/metabolismo , Isoleucina/análogos & derivados , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Imunidade Vegetal/genética , Pseudomonas syringae/patogenicidade , Metabolismo Secundário , Tiazóis/metabolismo , Fatores de Transcrição/metabolismo
12.
PLoS Genet ; 15(8): e1008013, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31437150

RESUMO

Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.


Assuntos
Hormônio Antimülleriano/genética , Esocidae/fisiologia , Cromossomos Sexuais/genética , Processos de Determinação Sexual/genética , Animais , Animais Geneticamente Modificados , Mapeamento Cromossômico , Feminino , Duplicação Gênica , Técnicas de Silenciamento de Genes , Masculino , Filogenia , Sintenia
13.
Int J Mol Sci ; 20(16)2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31416126

RESUMO

Mice bearing targeted gene mutations that affect the functions of natriuretic peptides (NPs) and natriuretic peptide receptors (NPRs) have contributed important information on the pathogenesis of hypertension, kidney disease, and cardiovascular dysfunction. Studies of mice having both complete gene disruption and tissue-specific gene ablation have contributed to our understanding of hypertension and cardiovascular disorders. These phenomena are consistent with an oligogenic inheritance in which interactions among a few alleles may account for genetic susceptibility to hypertension, renal insufficiency, and congestive heart failure. In addition to gene knockouts conferring increased risks of hypertension, kidney disorders, and cardiovascular dysfunction, studies of gene duplications have identified mutations that protect against high blood pressure and cardiovascular events, thus generating the notion that certain alleles can confer resistance to hypertension and heart disease. This review focuses on the intriguing phenotypes of Npr1 gene disruption and gene duplication in mice, with emphasis on hypertension and cardiovascular events using mouse models carrying Npr1 gene knockout and/or gene duplication. It also describes how Npr1 gene targeting in mice has contributed to our knowledge of the roles of NPs and NPRs in dose-dependently regulating hypertension and cardiovascular events.


Assuntos
Doenças Cardiovasculares/etiologia , Doenças Cardiovasculares/metabolismo , Variação Genética , Guanilato Ciclase/metabolismo , Receptores do Fator Natriurético Atrial/metabolismo , Animais , Biomarcadores , Doenças Cardiovasculares/diagnóstico , Modelos Animais de Doenças , Suscetibilidade a Doenças , Duplicação Gênica , Humanos , Hipertensão/diagnóstico , Hipertensão/etiologia , Hipertensão/metabolismo , Camundongos , Polimorfismo Genético , Disfunção Ventricular Esquerda , Remodelação Ventricular
14.
BMC Genomics ; 20(1): 635, 2019 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-31387534

RESUMO

BACKGROUND: As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. RESULTS: In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. CONCLUSIONS: Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1.


Assuntos
Brachypodium/genética , Genômica , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Sequência de Aminoácidos , Brachypodium/crescimento & desenvolvimento , Brachypodium/metabolismo , Sequência Conservada/genética , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Motivos de Nucleotídeos , Filogenia , Proteínas de Plantas/química , Sintenia , Fatores de Transcrição/química
15.
BMC Plant Biol ; 19(1): 344, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31390980

RESUMO

BACKGROUND: In the study, the trihelix family, also referred to as GT factors, is one of the transcription factor families. Trihelix genes play roles in the light response, seed maturation, leaf development, abiotic and biological stress and other biological activities. However, the trihelix family in tartary buckwheat (Fagopyrum tataricum), an important usable medicinal crop, has not yet been thoroughly studied. The genome of tartary buckwheat has recently been reported and provides a theoretical basis for our research on the characteristics and expression of trihelix genes in tartary buckwheat based at the whole level. RESULTS: In the present study, a total of 31 FtTH genes were identified based on the buckwheat genome. They were named from FtTH1 to FtTH31 and grouped into 5 groups (GT-1, GT-2, SH4, GTγ and SIP1). FtTH genes are not evenly distributed on the chromosomes, and we found segmental duplication events of FtTH genes on tartary buckwheat chromosomes. According to the results of gene and motif composition, FtTH located in the same group contained analogous intron/exon organizations and motif organizations. qRT-PCR showed that FtTH family members have multiple expression patterns in stems, roots, leaves, fruits, and flowers and during fruit development. CONCLUSIONS: Through our study, we identified 31 FtTH genes in tartary buckwheat and synthetically further analyzed the evolution and expression pattern of FtTH proteins. The structure and motif organizations of most genes are conserved in each subfamily, suggesting that they may be functionally conserved. The FtTH characteristics of the gene expression patterns indicate functional diversity in the time and space in the tartary buckwheat life process. Based on the discussion and analysis of FtTH gene function, we screened some genes closely related to the growth and development of tartary buckwheat. This will help us to further study the function of FtTH genes through experimental exploration in tartary buckwheat growth and improve the fruit of tartary buckwheat.


Assuntos
Fagopyrum/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/metabolismo , Mapeamento Cromossômico , Evolução Molecular , Fagopyrum/metabolismo , Duplicação Gênica , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genoma de Planta , Filogenia , Proteínas de Plantas/genética , Fatores de Transcrição/genética
16.
BMC Plant Biol ; 19(1): 347, 2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395025

RESUMO

BACKGROUND: Flavonoid 3'-hydroxlase (F3'H) is an important enzyme in determining the B-ring hydroxylation pattern of flavonoids. In monocots, previous studies indicated the presence of two groups of F3'Hs with different enzyme activities. One F3'H in rice was found to display novel chrysoeriol-specific 5'-hydroxylase activity. However, the evolutionary history of monocot F3'Hs and the molecular basis for the observed catalytic difference remained elusive. RESULTS: We performed genome-wide survey of 12 common monocot plants, and identified a total of 44 putative F3'H genes. The results showed that F3'H gene family had underwent volatile lineage-specific gene duplication and gene loss events in monocots. The expansion of F3'H gene family was mainly attributed to dispersed gene duplication. Phylogenetic analyses showed that monocot F3'Hs have evolved into two independent lineages (Class I and Class II) after gene duplication in the common ancestor of monocot plants. Evolutionary dynamics analyses had detected positive natural selection in Class II F3'Hs, acting on 7 specific amino acid sites. Protein modelling showed these selected sites were mainly located in the catalytic cavity of F3'H. Sequence alignment revealed that Class I and Class II F3'Hs displayed amino acid substitutions at two critical sites previously found to be responsible for F3'H and flavonoid 3'5'-hydroxylase (F3'5'H) activities. In addition, transcriptional divergence was also observed for Class I and Class II F3'Hs in four monocot species. CONCLUSIONS: We concluded that monocot F3'Hs have evolved into two independent lineages (Mono_F3'H Class I and Class II), after gene duplication during the common ancestor of monocot plants. The functional divergence of monocot F3'H Class II has been affected by positive natural selection, which acted on specific amino acid sites only. Critical amino acid sites have been identified to have high possibility to affect the substrate specificity of Class II F3'Hs. Our study provided an evolutionary and protein structural explanation to the previously observed chrysoeriol-specific 5'-hydroxylation activity for CYP75B4 in rice, which may also be true for other Class II F3'Hs in monocots. Our study presented clear evidence of plant-environmental interaction at the gene evolutionary level, and would guide future functional characterization of F3'Hs in cereal plants.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Grão Comestível/genética , Proteínas de Plantas/genética , Sistema Enzimático do Citocromo P-450/química , Grão Comestível/enzimologia , Evolução Molecular , Duplicação Gênica , Modelos Moleculares , Filogenia , Proteínas de Plantas/química , Seleção Genética , Alinhamento de Sequência
17.
Genes (Basel) ; 10(8)2019 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-31426485

RESUMO

Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar's circadian system and shed light on how the vertebrate circadian clock systems have evolved.


Assuntos
Peptídeos e Proteínas de Sinalização do Ritmo Circadiano/genética , Evolução Molecular , Proteínas de Peixes/genética , Peixes/genética , Animais , Fatores de Transcrição de Zíper de Leucina Básica/genética , Sequência Conservada , Peixes/classificação , Duplicação Gênica , Filogenia
18.
DNA Cell Biol ; 38(10): 1100-1111, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418589

RESUMO

Members of the Sox gene family play crucial roles during reproduction and development, but their genome-wide identification has not yet been performed in large yellow croaker, Larimichthys crocea. In this study, a total of 26 members of the Sox gene family were identified from the genome of large yellow croaker and classified into seven subgroups based on the conserved HMG-box domain they contain. Among the identified Sox gene family members, eight belonged to the SoxB subgroup (five in B1 and three in B2), four belonged to the SoxC subgroup, four belonged to the SoxD subgroup, six belonged to the SoxE subgroup, three belonged to the SoxF subgroup, and one belonged to the SoxK subgroup. During evolution, members of the SoxE subgroup (Sox8, Sox9, Sox10), Sox1, Sox4, Sox6, and Sox11 evolved into two copies, which may be a result of teleost-specific whole-genome duplication. Sox genes were distributed unevenly across 15 chromosomes. The number of introns in large yellow croaker Sox genes varied from 0 to 14. Results of the expression profile during embryogenesis revealed that most of the members of the Sox gene family had lower expression, except several Sox genes, and expression patterns also differed among each Sox gene group and duplicated gene. This study systematically characterized and analyzed the Sox gene family in large yellow croaker and provided new insights into its function during embryogenesis.


Assuntos
Proteínas de Peixes/genética , Regulação da Expressão Gênica no Desenvolvimento , Genoma , Perciformes/genética , Filogenia , Fatores de Transcrição SOXB1/genética , Sequência de Aminoácidos , Animais , Evolução Biológica , Mapeamento Cromossômico , Biologia Computacional , Embrião não Mamífero , Desenvolvimento Embrionário , Éxons , Proteínas de Peixes/classificação , Duplicação Gênica , Íntrons , Família Multigênica , Perciformes/classificação , Isoformas de Proteínas/classificação , Isoformas de Proteínas/genética , Fatores de Transcrição SOXB1/classificação , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
19.
BMC Genomics ; 20(1): 612, 2019 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-31349783

RESUMO

BACKGROUND: Nuclear Factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. The NF-Y transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a vital role in various biological processes in plants. However, the NF-Y gene family has not yet been reported from the peach genome. The current study identified and classified candidate peach NF-Y genes for further functional analysis of this family. RESULTS: The current study identified 24 Nuclear Factor Y (NF-Y) transcription factor subunits (6 NF-YA, 12 NF-YB, and 6 NF-YC subunits) in peach. These NF-Y subunits were described with respect to basic physicochemical characteristics, chromosome locations, gene structures, and conserved domains. Based on an analysis of the phylogenetic relationships among peach NF-Ys, six pairs of paralogous NF-Ys were detected. The expansion of the peach NF-Y family occurred by segmental and tandem duplication. Phylogenetic gene synteny of NF-Y proteins was observed between peach and Arabidopsis, and five pairs of paralogous NF-Y proteins from peach and Arabidopsis were identified. Twenty-four peach NF-Ys displayed a diversity of tissue expression patterns. In addition, drought-responsive cis-elements were observed in peach NF-Y promoters, and 9 peach NF-Y genes were shown to distinctly increase their transcript abundances under drought stress. CONCLUSIONS: This study identified 24 NF-Y genes in the peach genome and analysed their properties at different levels, providing a foundation for researchers to understand this gene family in peach. The up-regulation of 9 NF-Y genes under drought stress indicates that they can serve as candidate functional genes to further study drought resistance in peach.


Assuntos
Fator de Ligação a CCAAT/genética , Família Multigênica , Proteínas de Plantas/genética , Prunus persica/genética , Sequência de Aminoácidos , Arabidopsis/genética , Secas , Duplicação Gênica , Genoma de Planta , Filogenia , Estresse Fisiológico , Sintenia
20.
BMC Evol Biol ; 19(1): 156, 2019 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-31349784

RESUMO

BACKGROUND: The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ's complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fish family Poeciliidae, as members of this family vary markedly in their ability to supply nutrients to their offspring via a placenta. Here, we investigate the genomic basis underlying this phenotypic variation in Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes may have played a role in the evolution of the placenta in the Poeciliidae. RESULTS: We sequenced the genome of H. formosa, providing the first whole genome sequence for a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. Using comparative evolutionary analyses, we found 17 genes that were positively selected exclusively in H. formosa, as well as five gene duplications exclusive to H. formosa. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation. CONCLUSIONS: Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.


Assuntos
Evolução Biológica , Sequência Conservada , Ciprinodontiformes/genética , Genoma , Placenta/fisiologia , Animais , Feminino , Duplicação Gênica , Gravidez , Seleção Genética , Sequenciamento Completo do Genoma
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