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1.
BMC Plant Biol ; 21(1): 408, 2021 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-34493199

RESUMO

BACKGROUND: Mung bean (Vigna radiata) is a warm-season legume crop and belongs to the papilionoid subfamily of the Fabaceae family. China is the leading producer of mung bean in the world. Mung bean has significant economic and health benefits and is a promising species with broad adaptation ability and high tolerance to environmental stresses. OSCA (hyperosmolality-gated calcium-permeable channel) gene family members play an important role in the modulation of hypertonic stress, such as drought and salinity. However, genome-wide analysis of the OSCA gene family has not been conducted in mung bean. RESULTS: We identified a total of 13 OSCA genes in the mung bean genome and named them according to their homology with AtOSCAs. All the OSCAs were phylogenetically split into four clades. Phylogenetic relationship and synteny analyses showed that the VrOSCAs in mung bean and soybean shared a relatively conserved evolutionary history. In addition, three duplicated VrOSCA gene pairs were identified, and the duplicated VrOSCAs gene pairs mainly underwent purifying selection pressure during evolution. Protein domain, motif and transmembrane analyses indicated that most of the VrOSCAs shared similar structures with their homologs. The expression pattern showed that except for VrOSCA2.1, the other 12 VrOSCAs were upregulated under treatment with ABA, PEG and NaCl, among which VrOSCA1.4 showed the largest increased expression levels. The duplicated genes VrOSCA2.1/VrOSCA2.2 showed divergent expression, which might have resulted in functionalization during subsequent evolution. The expression profiles under ABA, PEG and NaCl stress revealed a functional divergence of VrOSCA genes, which agreed with the analysis of cis-acting regulatory elements in the promoter regions of VrOSCA genes. CONCLUSIONS: Collectively, the study provided a systematic analysis of the VrOSCA gene family in mung bean. Our results establish an important foundation for functional and evolutionary analysis of VrOSCAs and identify genes for further investigation of their ability to confer abiotic stress tolerance in mung bean.


Assuntos
Osmorregulação/genética , Proteínas de Plantas/genética , Vigna/fisiologia , Ácido Abscísico/farmacologia , Arabidopsis/genética , Duplicação Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genoma de Planta , Estudo de Associação Genômica Ampla , Família Multigênica , Oryza/genética , Pressão Osmótica , Filogenia , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas , Cloreto de Sódio/farmacologia , Soja/genética , Estresse Fisiológico/genética , Sintenia , Vigna/efeitos dos fármacos , Vigna/genética
2.
BMC Plant Biol ; 21(1): 413, 2021 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-34503442

RESUMO

BACKGROUND: In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. RESULTS: In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate  in pear fruits by real-time qRT-PCR. CONCLUSIONS: Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/genética , Proteínas de Plantas/genética , Pyrus/genética , Estresse Fisiológico/genética , Ácido Abscísico/farmacologia , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Cromossomos de Plantas , Éxons , Fragaria/genética , Frutas/genética , Frutas/crescimento & desenvolvimento , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Estudo de Associação Genômica Ampla , Íntrons , Família Multigênica , Filogenia , Proteínas de Plantas/metabolismo , Pyrus/efeitos dos fármacos , Salicilatos/farmacologia , Ácido Salicílico/farmacologia , Sintenia
3.
BMC Bioinformatics ; 22(Suppl 10): 394, 2021 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-34348661

RESUMO

BACKGROUND: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. RESULTS: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. CONCLUSIONS: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.


Assuntos
Evolução Molecular , Duplicação Gênica , Algoritmos , Genoma , Modelos Genéticos , Filogenia
4.
Biol Lett ; 17(9): 20210297, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34464540

RESUMO

The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy (Coprosma: 2x, Veronica: 6x) versus high-ploidy (Coprosma: 4-10x, Veronica: 12-18x) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.


Assuntos
Plantaginaceae , Rubiaceae , Veronica , Ecossistema , Duplicação Gênica , Nova Zelândia , Filogenia , Poliploidia
5.
BMC Genomics ; 22(1): 496, 2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34215180

RESUMO

BACKGROUND: Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process. RESULTS: We study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes. CONCLUSIONS: Our analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested.


Assuntos
Genoma Humano , Duplicações Segmentares Genômicas , Animais , Evolução Molecular , Duplicação Gênica , Genômica , Humanos
6.
BMC Plant Biol ; 21(1): 309, 2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210268

RESUMO

BACKGROUND: Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathway that control the balance between plant growth and stress response, but the functions of ZmSnRK2 in maize are rarely reported. Therefore, the study of ZmSnRK2 is of great importance to understand the ABA signaling pathways in maize. RESULTS: In this study, 14 ZmSnRK2 genes were identified in the latest version of maize genome database. Phylogenetic analysis revealed that ZmSnRK2s are divided into three subclasses based on their diversity of C-terminal domains. The exon-intron structures, phylogenetic, synteny and collinearity analysis indicated that SnRK2s, especially the subclass III of SnRK2, are evolutionally conserved in maize, rice and Arabidopsis. Subcellular localization showed that ZmSnRK2 proteins are localized in the nucleus and cytoplasm. The RNA-Seq datasets and qRT-PCR analysis showed that ZmSnRK2 genes exhibit spatial and temporal expression patterns during the growth and development of different maize tissues, and the transcript levels of some ZmSnRK2 genes in kernel are significantly induced by ABA and sucrose treatment. In addition, we found that ZmSnRK2.10, which belongs to subclass III, is highly expressed in kernel and activated by ABA. Overexpression of ZmSnRK2.10 partially rescued the ABA-insensitive phenotype of snrk2.2/2.3 double and snrk2.2/2.3/2.6 triple mutants and led to delaying plant flowering in Arabidopsis. CONCLUSION: The SnRK2 gene family exhibits a high evolutionary conservation and has expanded with whole-genome duplication events in plants. The ZmSnRK2s expanded in maize with whole-genome and segmental duplication, not tandem duplication. The expression pattern analysis of ZmSnRK2s in maize offers important information to study their functions. Study of the functions of ZmSnRK.10 in Arabidopsis suggests that the ABA-dependent members of SnRK2s are evolutionarily conserved in plants. Our study elucidated the structure and evolution of SnRK2 genes in plants and provided a basis for the functional study of ZmSnRK2s protein in maize.


Assuntos
Ácido Abscísico/metabolismo , Genes de Plantas , Transdução de Sinais , Zea mays/genética , Zea mays/metabolismo , Arabidopsis/genética , Sequência de Bases , Núcleo Celular/metabolismo , Cromossomos de Plantas/genética , Evolução Molecular , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Mutação/genética , Fenótipo , Filogenia , Transdução de Sinais/genética , Frações Subcelulares/metabolismo , Sintenia/genética
7.
BMC Plant Biol ; 21(1): 319, 2021 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-34217205

RESUMO

BACKGROUND: PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS: We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS: Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.


Assuntos
Genoma de Planta , Família Multigênica , Proteínas de Plantas/genética , Salinidade , Setaria (Planta)/genética , Setaria (Planta)/fisiologia , Cromossomos de Plantas/genética , Escherichia coli/metabolismo , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Anotação de Sequência Molecular , Motivos de Nucleotídeos/genética , Filogenia , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/metabolismo , Estresse Fisiológico/genética , Sintenia/genética
8.
Bioinformatics ; 37(Suppl_1): i133-i141, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252920

RESUMO

MOTIVATION: Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several consecutive domains are duplicated together as part of a single evolutionary event. Existing methods for inferring domain-level evolutionary events are based on reconciling domain trees with gene trees. While some formulations consider multiple domain duplications, they do not explicitly model tandem duplications; this leads to inaccurate inference of which domains duplicated together over the course of evolution. RESULTS: Here, we introduce a reconciliation-based framework that considers the relative positions of domains within extant sequences. We use this information to uncover tandem domain duplications within the evolutionary history of these genes. We devise an integer linear programming approach that solves our problem exactly, and a heuristic approach that works well in practice. We perform extensive simulation studies to demonstrate that our approaches can accurately uncover single and tandem domain duplications, and additionally test our approach on a well-studied orthogroup where lineage-specific domain expansions exhibit varying and complex domain duplication patterns. AVAILABILITY AND IMPLEMENTATION: Code is available on github at https://github.com/Singh-Lab/TandemDuplications. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Programação Linear , Evolução Molecular , Duplicação Gênica , Humanos , Filogenia , Domínios Proteicos
9.
Bioinformatics ; 37(Suppl_1): i120-i132, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252921

RESUMO

MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree. RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees. AVAILABILITY AND IMPLEMENTATION: EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.


Assuntos
Evolução Molecular , Transferência Genética Horizontal , Algoritmos , Duplicação Gênica , Genoma , Filogenia , Simbiose/genética
10.
Gene ; 799: 145840, 2021 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-34274467

RESUMO

In this study, 82 U-box genes were identified in wild emmer wheat (TdPUBs) through a genome-search method. Phylogenetic analysis classified them into seven groups and the genes belonging to the same group shared the similar exon-intron structure, motif organization and cis-element compositions. Synteny analysis of the U-box genes between different species revealed that segmental duplication and polyploidization mainly contributed to the expansion of TdPUBs. Furthermore, the genetic variations of U-box were investigated in wild emmer, domesticated emmer and durum wheat. Results showed that significant genetic bottleneck has occurred during domestication process of tetraploid emmer wheat. Meanwhile, 12 TdPUBs were co-located with known domestication related QTLs. Finally, the tissue-specific and stress-responsive TdPUB genes were identified through RNA-seq analysis. Combined with qPCR validation of 19 salt-responsive TdPUBs, the candidates involving in salt response were obtained. It lays the foundation to better understand the regulatory roles of U-box family in emmer wheat and beyond.


Assuntos
Filogenia , Proteínas de Plantas/genética , Triticum/genética , Cromossomos de Plantas , Produtos Agrícolas/genética , Domesticação , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Variação Genética , Genética Populacional , Genoma de Planta , Haplótipos , Família Multigênica , Sintenia , Tetraploidia
11.
J Mol Evol ; 89(6): 396-414, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34097121

RESUMO

The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.


Assuntos
Conversão Gênica , Genes Homeobox , Animais , Evolução Molecular , Duplicação Gênica , Genes Homeobox/genética , Genoma/genética , Mamíferos/genética , Filogenia , Coelhos
12.
Nat Commun ; 12(1): 3276, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078898

RESUMO

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.


Assuntos
Alcaloides de Berberina/metabolismo , Coptis/genética , Sistema Enzimático do Citocromo P-450/genética , Genoma de Planta , Proteínas de Plantas/genética , Vias Biossintéticas/genética , Coptis/química , Coptis/metabolismo , Sistema Enzimático do Citocromo P-450/metabolismo , Medicamentos de Ervas Chinesas , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/metabolismo , Plantas Medicinais
13.
Int J Mol Sci ; 22(9)2021 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-34066899

RESUMO

Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.


Assuntos
Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Gossypium/anatomia & histologia , Gossypium/genética , Pigmentação/genética , Proteínas de Plantas/genética , Cromossomos de Plantas/genética , Diploide , Duplicação Gênica , Perfilação da Expressão Gênica , Inativação Gênica , Genes de Plantas , Modelos Biológicos , Família Multigênica , Filogenia , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética , Sintenia/genética
14.
BMC Neurol ; 21(1): 243, 2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34171997

RESUMO

BACKGROUND: Hereditary motor and sensory neuropathy, also referred to as Charcot-Marie-Tooth disease (CMT), is most often caused by a duplication of the peripheral myelin protein 22 (PMP22) gene. This duplication causes CMT type 1A (CMT1A). CMT1A rarely occurs in combination with other hereditary neuromuscular disorders. However, such rare genetic coincidences produce a severe phenotype and have been reported in terms of "double trouble" overlapping syndrome. Waardenburg syndrome (WS) is the most common form of a hereditary syndromic deafness. It is primarily characterized by pigmentation anomalies and classified into four major phenotypes. A mutation in the SRY sex determining region Y-box 10 (SOX10) gene causes WS type 2 or 4 and peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, WS, and Hirschsprung disease. We describe a 11-year-old boy with extreme hypertrophic neuropathy because of a combination of CMT1A and WS type 2. This is the first published case on the co-occurrence of CMT1A and WS type 2. CASE PRESENTATION: The 11-year-old boy presented with motor developmental delay and a deterioration in unstable walking at 6 years of age. In addition, he had congenital hearing loss and heterochromia iridis. The neurological examination revealed weakness in the distal limbs with pes cavus. He was diagnosed with CMT1A by the fluorescence in situ hybridization method. His paternal pedigree had a history of CMT1A. However, no family member had congenital hearing loss. His clinical manifestation was apparently severe than those of his relatives with CMT1A. In addition, a whole-body magnetic resonance neurography revealed an extreme enlargement of his systemic cranial and spinal nerves. Subsequently, a genetic analysis revealed a heterozygous frameshift mutation c.876delT (p.F292Lfs*19) in the SOX10 gene. He was eventually diagnosed with WS type 2. CONCLUSIONS: We described a patient with a genetically confirmed overlapping diagnoses of CMT1A and WS type 2. The double trouble with the genes created a significant impact on the peripheral nerves system. Severe phenotype in the proband can be attributed to the cumulative effect of mutations in both PMP22 and SOX10 genes, responsible for demyelinating neuropathy.


Assuntos
Doença de Charcot-Marie-Tooth , Proteínas da Mielina/genética , Fatores de Transcrição SOXE/genética , Síndrome de Waardenburg , Doença de Charcot-Marie-Tooth/diagnóstico , Doença de Charcot-Marie-Tooth/genética , Criança , Doenças Desmielinizantes , Duplicação Gênica/genética , Humanos , Masculino , Mutação/genética , Síndrome de Waardenburg/diagnóstico , Síndrome de Waardenburg/genética
15.
Gene ; 795: 145782, 2021 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-34146634

RESUMO

Auxin/indole-3-acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root-specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT-qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA-mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish.


Assuntos
Regulação da Expressão Gênica de Plantas , Genes de Plantas , Ácidos Indolacéticos/imunologia , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/genética , Raphanus/crescimento & desenvolvimento , Raphanus/genética , Duplicação Gênica , Perfilação da Expressão Gênica , Ácidos Indolacéticos/metabolismo , Família Multigênica , Reação em Cadeia da Polimerase em Tempo Real
16.
Methods Mol Biol ; 2324: 3-18, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34165705

RESUMO

A pseudogene is defined as a genomic DNA sequence that looks like a mutated or truncated version of a known functional gene. Nearly four decades since their first discovery it has been estimated that between ~12,000 and ~20,000 pseudogenes exist in the human genome. Early efforts to characterize functions for pseudogenes were unsuccessful, thus they were considered functionless relics of evolutionary selection, junk DNA or genetic fossils. Remarkably, an increasing number of pseudogenes have been reported to be expressed as RNA transcripts above and beyond levels considered accidental or spurious transcription. There is emerging evidence that some expressed pseudogene transcripts have biological functions and should be defined as a subclass of functional long noncoding RNAs (lncRNA). In this introductory chapter, I briefly summarize the history and the current knowledge of pseudogenes, and highlight the emerging functions of some pseudogenes in human biology and disease. This second iteration of Pseudogenes in Methods in Molecular Biology highlights new methodological approaches to investigate this intriguing family of lncRNAs and the extent of their biological function.


Assuntos
Pseudogenes , RNA Longo não Codificante/genética , RNA Mensageiro/genética , Animais , Epigênese Genética , Evolução Molecular , Duplicação Gênica , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , Mutagênese Insercional , Mutação , Pseudogenes/genética , RNA Longo não Codificante/metabolismo , RNA Interferente Pequeno , Transcrição Genética
17.
Development ; 148(11)2021 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-34096572

RESUMO

Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.


Assuntos
Genes Homeobox/genética , Família Multigênica , Peixe-Zebra/genética , Peixe-Zebra/fisiologia , Animais , Sistemas CRISPR-Cas , Desenvolvimento Embrionário/genética , Evolução Molecular , Feminino , Duplicação Gênica , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Mutação , Esqueleto/anatomia & histologia , Esqueleto/crescimento & desenvolvimento , Especificidade da Espécie , Microtomografia por Raio-X , Peixe-Zebra/embriologia
18.
Int J Biol Macromol ; 185: 403-411, 2021 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-34166699

RESUMO

Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.


Assuntos
Rearranjo Gênico , Mantódeos/genética , Mitocôndrias/genética , RNA de Transferência/genética , Animais , Evolução Molecular , Duplicação Gênica , Ordem dos Genes , Genoma Mitocondrial , Conformação de Ácido Nucleico , Filogenia , Pseudogenes , RNA de Plantas/genética , RNA de Transferência/química , Análise de Sequência de DNA , Translocação Genética
19.
Nucleic Acids Res ; 49(12): 7088-7102, 2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34157109

RESUMO

RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase-α, ß, ß'. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the ß or ß' subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.


Assuntos
Bacillus subtilis/enzimologia , Bacillus subtilis/genética , Endorribonucleases/fisiologia , RNA Mensageiro/metabolismo , RNA Polimerases Dirigidas por DNA/química , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Endorribonucleases/genética , Evolução Molecular , Deleção de Genes , Duplicação Gênica , Genes Bacterianos , Homeostase , Mutação , Supressão Genética , Transcrição Genética , Transcriptoma
20.
Int J Mol Sci ; 22(11)2021 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-34067314

RESUMO

Cholinergic α7 nicotinic receptors encoded by the CHRNA7 gene are ligand-gated ion channels directly related to memory and immunomodulation. Exons 5-7 in CHRNA7 can be duplicated and fused to exons A-E of FAR7a, resulting in a hybrid gene known as CHRFAM7A, unique to humans. Its product, denoted herein as Dupα7, is a truncated subunit where the N-terminal 146 residues of the ligand binding domain of the α7 receptor have been replaced by 27 residues from FAM7. Dupα7 negatively affects the functioning of α7 receptors associated with neurological disorders, including Alzheimer's diseases and schizophrenia. However, the stoichiometry for the α7 nicotinic receptor containing dupα7 monomers remains unknown. In this work, we developed computational models of all possible combinations of wild-type α7 and dupα7 pentamers and evaluated their stability via atomistic molecular dynamics and coarse-grain simulations. We assessed the effect of dupα7 subunits on the Ca2+ conductance using free energy calculations. We showed that receptors comprising of four or more dupα7 subunits are not stable enough to constitute a functional ion channel. We also showed that models with dupα7/α7 interfaces are more stable and are less detrimental for the ion conductance in comparison to dupα7/dupα7 interfaces. Based on these models, we used protein-protein docking to evaluate how such interfaces would interact with an antagonist, α-bungarotoxin, and amyloid Aß42. Our findings show that the optimal stoichiometry of dupα7/α7 functional pentamers should be no more than three dupα7 monomers, in favour of a dupα7/α7 interface in comparison to a homodimer dupα7/dupα7 interface. We also showed that receptors bearing dupα7 subunits are less sensitive to Aß42 effects, which may shed light on the translational gap reported for strategies focused on nicotinic receptors in 'Alzheimer's disease research.


Assuntos
Doenças do Sistema Nervoso/genética , Doenças do Sistema Nervoso/metabolismo , Receptores Nicotínicos/genética , Receptores Nicotínicos/metabolismo , Receptor Nicotínico de Acetilcolina alfa7/genética , Receptor Nicotínico de Acetilcolina alfa7/metabolismo , Animais , Éxons/genética , Duplicação Gênica/genética , Humanos , Ligantes , Camundongos
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