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1.
RNA ; 26(10): 1464-1480, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32631843

RESUMO

Many eukaryotes use RNA processing, including alternative splicing, to express multiple gene products from the same gene. The budding yeast Saccharomyces cerevisiae has been successfully used to study the mechanism of splicing and the splicing machinery, but alternative splicing in yeast is relatively rare and has not been extensively studied. Alternative splicing of SKI7/HBS1 is widely conserved, but yeast and a few other eukaryotes have replaced this one alternatively spliced gene with a pair of duplicated, unspliced genes as part of a whole genome doubling (WGD). We show that other examples of alternative splicing known to have functional consequences are widely conserved within Saccharomycotina. A common mechanism by which alternative splicing has disappeared is by replacement of an alternatively spliced gene with duplicate unspliced genes. This loss of alternative splicing does not always take place soon after duplication, but can take place after sufficient time has elapsed for speciation. Saccharomycetaceae that diverged before WGD use alternative splicing more frequently than S. cerevisiae, suggesting that WGD is a major reason for infrequent alternative splicing in yeast. We anticipate that WGDs in other lineages may have had the same effect. Having observed that two functionally distinct splice-isoforms are often replaced by duplicated genes allowed us to reverse the reasoning. We thereby identify several splice isoforms that are likely to produce two functionally distinct proteins because we find them replaced by duplicated genes in related species. We also identify some alternative splicing events that are not conserved in closely related species and unlikely to produce functionally distinct proteins.


Assuntos
Processamento Alternativo/genética , Proteoma/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Saccharomycetales/genética , Proteínas Adaptadoras de Transdução de Sinal/genética , Evolução Molecular , Duplicação Gênica/genética , Genoma/genética , Isoformas de Proteínas/genética
2.
Hum Genet ; 139(11): 1417-1427, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32488466

RESUMO

An inverted duplication with a terminal deletion (inv-dup-del) is one of the complex constitutional structural rearrangements that can occur in a chromosome. Although breakages of dicentric chromosome have been suggested, the precise mechanism of this is yet to be fully understood. In our present study, we investigated the genomic structure of 10 inv-dup-del cases to elucidate this mechanism. Two recurrent 8p inv-dup-del cases harbored a large copy-number-neutral region between the duplication and deletion in common. Although the other non-recurrent cases did not appear to have this copy-number-neutral region, refined sequencing analysis identified that they contained a small intervening region at the junction between the inverted and non-inverted segment. The size of this small intervening region ranged from 1741 to 3728 bp. Combined with a presence of microhomology at the junction, a resolution of the replication fork stalling through template switching within the same replication fork is suggested. We further observed two cases with mosaicism of the dicentric chromosome and various structural rearrangements related to the dicentric chromosome. Refined analysis allowed us to identify different breakpoints on the same chromosome in the same case, implicating multiple rounds of U-type formation and its breakage. From these results, we propose that a replication-based mechanism generates unstable dicentric chromosomes and that their breakage leads to the formation of inv-dup-dels and other related derivative chromosomes.


Assuntos
Transtornos Cromossômicos/genética , Inversão Cromossômica/genética , Cromossomos/genética , Duplicação Gênica/genética , Deleção de Sequência/genética , Deleção Cromossômica , Replicação do DNA/genética , Humanos , Mosaicismo
3.
Gene ; 753: 144777, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32428695

RESUMO

As a crucial member of the Forkhead Box family, class O (FoxO) plays an essential role in growth, cell differentiation, metabolism, immunization, and apoptosis. Meanwhile, FoxO3 is the primary regulator and effective inhibitor of primordial follicle activation. In this study, seven foxo genes were identified in black rockfish (Sebastes schlegelii), including two foxo1 genes (foxo1a, foxo1b), two foxo3 genes (foxo3, foxo3l), one foxo4 gene, and two foxo6 genes (foxo6a, foxo6b). foxo3l was derived from teleost-specific whole-genome duplication events. Evaluation of tissue expression pattern revealed that foxo3l displayed sexually dimorphic expression with a high level in the ovary and spatial expression only in the cytoplasm of follicle cells and oocytes. When the ovaries were stimulated by estrogen and gonadotropin, foxo3l expression was remarkably reduced, and the effect of androgen was completely different. We considered that foxo3l lost its ability to inhibit follicular precocity because of mass ovulation by hormone stimulation, resulting in its decreased expression. Such evidence indicated that foxo3l is an important regulator of reproduction-related functions in black rockfish. This study provides new insights into foxo3l genes for further functional research in teleost.


Assuntos
Proteína Forkhead Box O3/genética , Perciformes/genética , Sequência de Aminoácidos , Animais , Feminino , Doenças dos Peixes/imunologia , Proteínas de Peixes/genética , Proteína Forkhead Box O3/metabolismo , Fatores de Transcrição Forkhead/genética , Duplicação Gênica/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/genética , Imunidade Inata/genética , Oócitos/metabolismo , Oogênese/genética , Ovário/metabolismo , Filogenia , Alinhamento de Sequência
4.
Gene ; 753: 144816, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32473250

RESUMO

Hemizygosity of the MIR17HG gene encoding the miR-17 ~ 92 cluster is associated with Feingold syndrome 2 characterized by intellectual disability, skeletal abnormalities, short stature, and microcephaly. Here, we report on a female with a de novo 13q31.3 microduplication encompassing MIR17HG but excluding GPC5. She presented developmental delay, skeletal and digital abnormalities, and features such as tall stature and macrocephaly mirroring those of Feingold syndrome 2 patients. The limited extent of the proband's rearrangement to the miR cluster and the corresponding normal expression level of the neighboring GPC5 in her cells, together with previously described data on affected individuals of two families carrying overlapping duplications of the miR-17 ~ 92 cluster that comprise part of GPC5, who likewise presented macrocephaly, developmental delay, as well as skeletal, digital and stature abnormalities, allow to define a new syndrome due to independent microduplication of the miR-17 ~ 92 cluster.


Assuntos
Transtornos Cromossômicos/genética , Pálpebras/anormalidades , Deficiência Intelectual/genética , Deformidades Congênitas dos Membros/genética , MicroRNAs/genética , Microcefalia/genética , Fístula Traqueoesofágica/genética , Adolescente , Deleção Cromossômica , Cromossomos Humanos Par 13/genética , Hibridização Genômica Comparativa/métodos , Deficiências do Desenvolvimento/genética , Nanismo/genética , Feminino , Duplicação Gênica/genética , Glipicanas/genética , Glipicanas/metabolismo , Humanos , Fenótipo
6.
PLoS Genet ; 16(3): e1008615, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32130223

RESUMO

The relative linear order of most genes on bacterial chromosomes is not conserved over evolutionary timescales. One explanation is that selection is weak, allowing recombination to randomize gene order by genetic drift. However, most chromosomal rearrangements are deleterious to fitness. In contrast, we propose the hypothesis that rearrangements in gene order are more likely the result of selection during niche adaptation (SNAP). Partial chromosomal duplications occur very frequently by recombination between direct repeat sequences. Duplicated regions may contain tens to hundreds of genes and segregate quickly unless maintained by selection. Bacteria exposed to non-lethal selections (for example, a requirement to grow on a poor nutrient) can adapt by maintaining a duplication that includes a gene that improves relative fitness. Further improvements in fitness result from the loss or inactivation of non-selected genes within each copy of the duplication. When genes that are essential in single copy are lost from different copies of the duplication, segregation is prevented even if the original selection is lifted. Functional gene loss continues until a new genetic equilibrium is reached. The outcome is a rearranged gene order. Mathematical modelling shows that this process of positive selection to adapt to a new niche can rapidly drive rearrangements in gene order to fixation. Signature features (duplication formation and divergence) of the SNAP model were identified in natural isolates from multiple species showing that the initial two steps in the SNAP process can occur with a remarkably high frequency. Further bioinformatic and experimental analyses are required to test if and to which extend the SNAP process acts on bacterial genomes.


Assuntos
Aclimatação/genética , Cromossomos Bacterianos/genética , Duplicação Gênica/genética , Rearranjo Gênico/genética , Seleção Genética/genética , Aberrações Cromossômicas , Evolução Molecular , Frequência do Gene/genética , Ordem dos Genes/genética , Genoma Bacteriano/genética , Modelos Teóricos , Filogenia
7.
PLoS One ; 15(2): e0228877, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32050009

RESUMO

The efflux pumps from the Resistance-Nodulation-Division family, RND, are main contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the MdtABC pump is unusual by having two inner membrane components. The two components, MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the MdtBC pumps in the context of other RNDs. We show that the individual inner membrane components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their existence is a result of a single gene duplication. We argue that this gene duplication was an ancient event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa share a close common ancestor, suggesting the MexMN pump arose by another gene duplication event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core bacterial efflux pump repertoires have been generally stable throughout the course of evolution.


Assuntos
Proteínas de Bactérias/genética , Duplicação Gênica/genética , Proteobactérias/genética , Pseudomonas aeruginosa/genética , Farmacorresistência Bacteriana Múltipla/genética , Proteínas de Membrana Transportadoras/genética , Filogenia
8.
J Glaucoma ; 29(5): 331-336, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32079994

RESUMO

PRéCIS:: One (0.2%) of 418 Korean normal-tension glaucoma (NTG) patients had TBK1 duplication. The putative mechanism of TBK1 duplication in Korean NTG patients is the nonhomologous end-joining. PURPOSE: TBK1 duplication is a genomic cause of familial NTG. NTG accounts for up to 90% of primary open-angle glaucoma in Koreans, with genetic tendency. We aimed to investigate the prevalence of TBK1 duplication in Korean NTG patients and to identify their genomic structure and duplication mechanism. MATERIALS AND METHODS: We obtained DNA samples from 418 NTG patients and 195 healthy controls for evaluating TBK1 copy number variations using a semiquantitative polymerase chain reaction (PCR). The samples with TBK1 gene duplication were further confirmed using droplet digital PCR. The whole-genome sequencing of patient samples with duplications was performed to identify the accurate breakpoints and to elucidate the genomic structure. Ophthalmic evaluation and confirmation of TBK1 duplication using junction PCR were performed in families of positive patients. RESULTS: TBK1 duplication was found in 1 of 418 NTG cases (0.2%). The duplication range was from g.64,803,151 to g.64,927,214 (124,063 bp). It is the smallest region of overlapping duplication in TBK1. Any repetitive sequences were not found near the breakpoints of our case. Inserted sequences were found within the breakpoints. A brother and a niece of the positive case appeared the typical clinical features of NTG and shared the same TBK1 duplications with the index case. CONCLUSIONS: In Korea, the prevalence of TBK1 duplication was 0.2% and the smallest reported TBK1 duplication associated with NTG was found. The mechanism of TBK1 duplication was suggested to be nonhomologous end-joining while a previous report pointed out the mechanism of TBK1 duplications as nonallelic homologous recombination.


Assuntos
Duplicação Gênica/genética , Predisposição Genética para Doença/genética , Glaucoma de Baixa Tensão/genética , Proteínas Serina-Treonina Quinases/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Grupo com Ancestrais do Continente Asiático/genética , DNA/genética , Variações do Número de Cópias de DNA , Feminino , Humanos , Pressão Intraocular , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase Multiplex , República da Coreia/epidemiologia , Sequenciamento Completo do Genoma , Adulto Jovem
9.
BMC Genomics ; 21(1): 12, 2020 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-31900112

RESUMO

BACKGROUND: Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. RESULTS: In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. CONCLUSION: These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.


Assuntos
Embriófitas/genética , Genômica , Proteínas de Plantas/genética , Estresse Fisiológico/genética , Arabidopsis/genética , Cromossomos de Plantas/genética , Duplicação Gênica/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta/genética , Filogenia , Alinhamento de Sequência
10.
Am J Ophthalmol ; 214: 52-62, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-31987900

RESUMO

PURPOSE: To characterize features of glaucoma associated with a TANK binding kinase 1 (TBK1) gene duplication, which is among the most common molecularly defined causes of normal tension glaucoma (NTG). DESIGN: Retrospective observational case series. METHODS: We conducted a retrospective case series, by reviewing medical records of 7 members of a pedigree with NTG caused by TBK1 gene duplications. Clinical features of these patients at diagnosis, throughout management, and at latest follow-up were identified, including age, intraocular pressure (IOP), central corneal thickness (CCT), optic nerve head appearance, and mean deviation (MD) assessed with Humphrey visual field (HVF) testing protocols. RESULTS: At initial diagnosis, the mean age was 35 ± 7 years, IOP was 16 ± 2.1 mm Hg, cup-to-disc (C/D) ratio was 0.9 ± 0.08, and MD assessed via HVF 30-2 and/or 24-2 testing protocols was -9.0 ± 8.9 (range: -1.8 to -27) dB in the 14 study eyes. At initial diagnosis, 4 of 14 eyes (28%) had no visual field defect, 4 (28%) had early visual field defects, and 6 (43%) had severe visual field defects. Patients had a mean follow-up of 21.5 ± 9.0 years and experienced an average reduction of IOP by 28%. Four of 12 eyes (33%) had stable visual fields throughout follow-up, while 8 eyes (67%) had slow-to-moderate progression. The 30-2 and/or 24-2 HVF tests had an average change in MD of -0.53 ± 0.26 dB/year. No eyes had rapid progression with an MD >1.0 dB/year. At final follow-up, the mean IOP was 11.5 ± 2.9, and C/D ratio was 0.94 ± 0.4. At final follow-up, 3 of 14 eyes (21%) had early visual field defects, 4 (29%) had moderate visual field defects, and 7 (50%) had severe visual field defects. Six of 14 eyes (43%) met criteria for legal blindness. CONCLUSIONS: We provide the first report of the clinical features and long-term clinical course in a family of NTG patients with TBK1 gene duplications. TBK1-associated glaucoma exhibits classic features of NTG. Patients present with severe disease at a relatively early age and most (67%) have slow-to-moderate progression of their visual field defects. The rate of visual field change appears correlated with the magnitude of IOP, suggesting that it may be advantageous to set extremely low IOP targets for some patients with TBK1-associated glaucoma.


Assuntos
Duplicação Gênica/genética , Glaucoma de Baixa Tensão/genética , Mutação/genética , Proteínas Serina-Treonina Quinases/genética , Adulto , Idoso , Feminino , Seguimentos , Humanos , Pressão Intraocular/fisiologia , Glaucoma de Baixa Tensão/diagnóstico , Masculino , Pessoa de Meia-Idade , Linhagem , Estudos Retrospectivos , Tonometria Ocular , Transtornos da Visão/diagnóstico , Transtornos da Visão/genética , Testes de Campo Visual , Campos Visuais/fisiologia , Adulto Jovem
11.
Planta ; 251(2): 55, 2020 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-31974682

RESUMO

MAIN CONCLUSION: Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increase the functional diversification of MIR169 in tomato. MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.


Assuntos
Variação Genética , Lycopersicon esculentum/genética , MicroRNAs/genética , Arabidopsis/genética , Sequência de Bases , Evolução Molecular , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , MicroRNAs/metabolismo , Oryza/genética , Desenvolvimento Vegetal/genética , Regiões Promotoras Genéticas , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Reprodutibilidade dos Testes , Especificidade da Espécie , Estresse Fisiológico/genética , Tabaco/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
12.
Nucleic Acids Res ; 48(2): 761-769, 2020 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-31777935

RESUMO

Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using genetic assays and mutation accumulation lines, we find that point mutations in topA increase the rate of sequence deletion and duplication events. Interestingly, we observe that a single residue substitution (R168C) results in a high rate of head-to-tail (tandem) short sequence duplications, which are independent of existing sequence repeats. Finally, we show that the unique mutation spectrum of topA mutants enhances the emergence of antibiotic resistance in comparison to mismatch-repair (mutS) mutators, and leads to new resistance genotypes. Our findings highlight a potential link between the catalytic activity of topoisomerases and the fundamental question regarding the emergence of de novo tandem repeats, which are known modulators of bacterial evolution.


Assuntos
Dióxido de Carbono/metabolismo , DNA Topoisomerases Tipo I/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Proteína MutS de Ligação de DNA com Erro de Pareamento/genética , Biomassa , Dióxido de Carbono/química , DNA Topoisomerases Tipo I/química , Farmacorresistência Bacteriana/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Evolução Molecular , Duplicação Gênica/genética , Genótipo , Proteína MutS de Ligação de DNA com Erro de Pareamento/química , Mutação , Mutação Puntual/genética
13.
Genes (Basel) ; 10(11)2019 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-31717396

RESUMO

Prunus mume, which is a rosaceous arbor with very high ornamental, edible and medical values, has a distribution that is mainly restricted by low temperature. WRKY transcription factor genes play crucial roles in the growth, development, and stress responses of plants. However, the WRKY gene family has not been characterised in P. mume. There were 58 PmWRKYs identified from genome of P. mume. They were anchored onto eight link groups and categorised into three broad groups. The gene structure and motif composition were reasonably conservative in each group. Investigation of gene duplication indicated that nine and seven PmWRKYs were arranged in tandem and segmental duplications, respectively. PmWRKYs were discriminately expressed in different tissues (i.e., roots, stems, leaves, flowers and fruits) in P. mume. The 17 cold-related candidate genes were selected based on RNA-seq data. Further, to investigate the function of PmWRKYs in low temperatures, the expression patterns under artificial cold treatments were analysed. The results showed that the expression levels of the 12 PmWRKYs genes significantly and 5 genes slightly changed in stems. In particular, the expression level of PmWRKY18 was up-regulated after ABA treatment. In addition, the spatiotemporal expression patterns of 17 PmWRKYs were analysed in winter. These results indicated that 17 PmWRKYs were potential transcription factors regulating cold resistance in P. mume.


Assuntos
Resposta ao Choque Frio/genética , Prunus/genética , Fatores de Transcrição/genética , Cromossomos de Plantas/genética , Temperatura Baixa , Sequência Conservada/genética , Duplicação Gênica/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Família Multigênica/genética , Filogenia , Proteínas de Plantas/genética , Fatores de Transcrição/metabolismo
14.
Genes (Basel) ; 10(11)2019 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-31671601

RESUMO

Sex chromosomes in some reptiles share synteny with distantly related amniotes in regions orthologous to squamate chromosome 2. The latter finding suggests that chromosome 2 was formerly part of a larger ancestral (amniote) super-sex chromosome and raises questions about how sex chromosomes are formed and modified in reptiles. Australian dragon lizards (Agamidae) are emerging as an excellent model for studying these processes. In particular, they exhibit both genotypic (GSD) and temperature-dependent (TSD) sex determination, show evidence of transitions between the two modes and have evolved non-homologous ZW sex microchromosomes even within the same evolutionary lineage. They therefore represent an excellent group to probe further the idea of a shared ancestral super-sex chromosome and to investigate mechanisms for transition between different sex chromosome forms. Here, we compare sex chromosome homology among eight dragon lizard species from five genera to identify key cytological differences and the mechanisms that may be driving sex chromosome evolution in this group. We performed fluorescence in situ hybridisation to physically map bacterial artificial chromosome (BAC) clones from the bearded dragon, Pogona vitticeps' ZW sex chromosomes and a nucleolar organising region (NOR) probe in males and females of eight Agamid species exhibiting either GSD or TSD. We show that the sex chromosome derived BAC clone hybridises near the telomere of chromosome 2q in all eight species examined. This clone also hybridises to the sex microchromosomes of three species (P vitticeps, P. barbata and Diporiphora nobbi) and a pair of microchromosomes in three others (Ctenophorus pictus, Amphibolurus norrisi and Amphibolurus muricatus). No other chromosomes are marked by the probe in two species from the closely related genus Physignathus. A probe bearing nucleolar organising region (NOR) sequences maps close to the telomere of chromosome 2q in all eight species, and to the ZW pair in P. vitticeps and P. barbata, the W microchromosome in D. nobbi, and several microchromosomes in P. cocincinus. Our findings provide evidence of sequence homology between chromosome 2 and the sex chromosomes of multiple agamids. These data support the hypothesis that there was an ancestral sex chromosome in amniotes that gave rise to squamate chromosome 2 and raises the prospect that some particular property of this chromosome has favoured its role as a sex chromosome in amniotes. It is likely that the amplification of repetitive sequences associated with this region has driven the high level of heterochromatinisation of the sex-specific chromosomes in three species of agamid. Our data suggest a possible mechanism for chromosome rearrangement, including inversion and duplication near the telomeric regions of the ancestral chromosome 2 and subsequent translocation to the ZW sex microchromosomes in three agamid species. It is plausible that these chromosome rearrangements involving sex chromosomes also drove speciation in this group.


Assuntos
Iguanas/genética , Região Organizadora do Nucléolo/genética , Cromossomos Sexuais/genética , Animais , Austrália , Evolução Biológica , Estruturas Cromossômicas/genética , Evolução Molecular , Feminino , Duplicação Gênica/genética , Hibridização in Situ Fluorescente , Cariotipagem/métodos , Lagartos/genética , Masculino , Região Organizadora do Nucléolo/fisiologia , Sequências Repetitivas de Ácido Nucleico/genética , Homologia de Sequência , Análise para Determinação do Sexo/métodos , Telômero/genética , Translocação Genética/genética
15.
BMC Genomics ; 20(1): 772, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31651257

RESUMO

BACKGROUND: Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. RESULTS: In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response. CONCLUSIONS: These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.


Assuntos
Evolução Molecular , Genômica , Fatores de Transcrição de Choque Térmico/genética , Raphanus/genética , Raphanus/fisiologia , Estresse Fisiológico/genética , Cromossomos de Plantas/genética , Sequência Conservada , Éxons/genética , Duplicação Gênica/genética , Íntrons/genética , Motivos de Nucleotídeos/genética , Filogenia
16.
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
17.
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
18.
BMC Genomics ; 20(1): 694, 2019 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-31477007

RESUMO

BACKGROUND: Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important traits in aquaculture and the evolutionary consequences of whole genome duplications. Although genome assemblies now exist for a number of salmonid species, the lack of regulatory annotations are holding back our mechanistic understanding of how genetic variation in non-coding regulatory regions affect gene expression and the downstream phenotypic effects. RESULTS: We present SalMotifDB, a database and associated web and R interface for the analysis of transcription factors (TFs) and their cis-regulatory binding sites in five salmonid genomes. SalMotifDB integrates TF-binding site information for 3072 non-redundant DNA patterns (motifs) assembled from a large number of metazoan motif databases. Through motif matching and TF prediction, we have used these multi-species databases to construct putative regulatory networks in salmonid species. The utility of SalMotifDB is demonstrated by showing that key lipid metabolism regulators are predicted to regulate a set of genes affected by different lipid and fatty acid content in the feed, and by showing that our motif database explains a significant proportion of gene expression divergence in gene duplicates originating from the salmonid specific whole genome duplication. CONCLUSIONS: SalMotifDB is an effective tool for analyzing transcription factors, their binding sites and the resulting gene regulatory networks in salmonid species, and will be an important tool for gaining a better mechanistic understanding of gene regulation and the associated phenotypes in salmonids. SalMotifDB is available at https://salmobase.org/apps/SalMotifDB .


Assuntos
Bases de Dados Genéticas , Genômica/métodos , Salmonidae/genética , Fatores de Transcrição/metabolismo , Animais , DNA/química , Duplicação Gênica/genética , Redes Reguladoras de Genes , Metabolismo dos Lipídeos/genética , Motivos de Nucleotídeos , Ligação Proteica
19.
Biomed Res Int ; 2019: 8620878, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31321242

RESUMO

CCN gene family members have recently been identified as multifunctional regulators involved in diverse biological functions, especially in vascular and skeletal development. In the present study, a comparative genomic and phylogenetic analysis was performed to show the similarities and differences in structure and function of CCNs from different organisms and to reveal their potential evolutionary relationship. First, CCN homologs of metazoans from different species were identified. Then we made multiple sequence alignments, MEME analysis, and functional sites prediction, which show the highly conserved structural features among CCN metazoans. The phylogenetic tree was further established, and thus CCNs were found undergoing extensive lineage-specific duplication events and lineage-specific expansion during the evolutionary process. Besides, comparative analysis about the genomic organization and chromosomal CCN gene surrounding indicated a clear orthologous relationship among these species counterparts. At last, based on these research results above, a potential evolutionary scenario was generated to overview the origin and evolution of the CCN gene family.


Assuntos
Proteínas de Sinalização Intercelular CCN/genética , Evolução Molecular , Genômica , Filogenia , Sequência de Aminoácidos/genética , Animais , Proteínas de Sinalização Intercelular CCN/classificação , Duplicação Gênica/genética , Íntrons/genética , Família Multigênica , Alinhamento de Sequência
20.
Sci Adv ; 5(6): eaav0547, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31249862

RESUMO

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a "Wakin" goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.


Assuntos
Duplicação Gênica/genética , Genoma/genética , Carpa Dourada/genética , Animais , Ásia , Carpas/genética , Evolução Molecular , Éxons/genética , Genômica/métodos , Genótipo , Fenótipo , Peixe-Zebra/genética
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