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1.
Cytogenet Genome Res ; 158(3): 160-169, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31394537

RESUMO

The discovery of sex chromosome systems in non-model organisms has elicited growing recognition that sex chromosomes evolved via diverse paths that are not fully elucidated. Lineages with labile sex determination, such as turtles, hold critical cues, yet data are skewed toward hide-neck turtles (suborder Cryptodira) and scant for side-neck turtles (suborder Pleurodira). Here, we used classic and molecular cytogenetics to investigate Emydura subglobosa (ESU), an unstudied side-neck turtle with genotypic sex determination from the family Chelidae, where extensive morphological divergence exists among XX/XY systems. Our data represent the first cytogenetic description for ESU. Similarities were found between ESU and E. macquarii (EMA), such as identical chromosome number (2n = 50), a single and dimorphic nucleolus organizer region (NOR) localized in a microchromosome pair (ESU14) of both sexes (detected via FISH of 18S rDNA). Only the larger NOR is active (detected by silver staining). As in EMA, comparative genome hybridization revealed putative macro XX/XY chromosomes in ESU (the 4th largest pair). Our comparative analyses and revaluation of previous data strongly support the hypothesis that Emydura's XX/XY system evolved via fusion of an ancestral micro-Y (retained by Chelodina longicollis) onto a macro-autosome. This evolutionary trajectory differs from the purported independent evolution of XX/XY from separate ancestral autosomes in Chelodina and Emydura that was previously reported. Our data permit dating this Y-autosome fusion to at least the split of Emydura around 45 Mya and add critical information about the evolution of the remarkable diversity of sex-determining mechanisms in turtles, reptiles, and vertebrates.


Assuntos
Evolução Molecular , Cromossomos Sexuais/genética , Tartarugas/genética , Animais , Hibridização Genômica Comparativa , Hibridização in Situ Fluorescente , Cariótipo , Masculino , Repetições de Microssatélites/genética , RNA Ribossômico 18S/genética , Coloração pela Prata , Tartarugas/classificação
2.
Gene ; 716: 144036, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31381952

RESUMO

Nebulin is a 770 kDa protein that is localized along the thin filaments of skeletal muscles in vertebrates. It is also present in the striated muscles of Amphioxus, an invertebrate cephalochordate that is phylogenetically close to vertebrates. However, the nebulin of urochordate ascidians or its expression in invertebrate hearts has not been investigated. In this study, we investigated the structure and cardiac expression of the nebulin gene in Ciona intestinalis, a urochordate whose phylogeny lies between cephalochordates and vertebrates. As a result of the gene structure analysis, we found that the Ciona nebulin gene predicted to be 62 kb and consists of 143 exons. The nebulin was expected to consist of a unique N-terminal region, followed by 155 nebulin repeats, another unique region, a Ser-rich region and a C-terminal SH3 domain. Whole-mount in situ hybridization experiments showed that the Ciona nebulin gene was expressed in a variety of muscles, including hearts. However, Western blot analysis using antibody to Ciona nebulin did not detect the presence of full-length nebulin. Alternatively, RT-PCR experiments on samples of Ciona heart detected the expression of nebulette-like and nrap-like isoforms from the Ciona nebulin gene. These results indicate that, similarly to vertebrate hearts, Ciona hearts do not express nebulin, but rather nrap- and nebulette-like isoforms. These results also imply that the nebulin, nebulette and nrap genes in vertebrates were separated from an ancestral invertebrate nebulin gene during vertebrate evolution.


Assuntos
Ciona intestinalis/genética , Família Multigênica , Proteínas Musculares/genética , Miocárdio/metabolismo , Animais , Ciona intestinalis/metabolismo , Evolução Molecular , Éxons , Íntrons , Proteínas Musculares/química , Proteínas Musculares/metabolismo , Domínios Proteicos , RNA Mensageiro/metabolismo
3.
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
4.
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
5.
BMC Plant Biol ; 19(1): 353, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31412775

RESUMO

BACKGROUND: The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poorly understood. RESULTS: Cultivated soybean (Glycine max) was domesticated from wild soybean (Glycine soja). To illuminate their roles in this evolutionary process, we comparatively investigated the G. max PHO1 genes (GmPHO1) in Suinong 14 (SN14) and G. soja PHO1 genes (GsPHO1) in ZYD00006 (ZYD6). The sequences of the orthologous Gm-GsPHO1 pairs were grouped into two Classes. The expression of Class I in both SN14 and ZYD6 was widely but relatively high in developing fruits, whereas Class II was predominantly expressed in the roots. The whole family displayed diverse response patterns to salt stresses and Pi-starvation in roots. Between SN14 and ZYD6, most PHO1 genes responded similarly to salinity stresses, and half had sharp contrasts in response to Pi-starvation, which corroborated the differential response capacities to salinity and low-Pi stress between SN14 and ZYD6. Furthermore, in transgenic Arabidopsis plants, most Class II members and GmPHO1;H9 from Class I could enhance salt tolerance, while only two Class II genes (GmPHO1;H4 and GmPHO1;H8) differently altered sensitivity to Pi-starvation. The expression of critical genes was accordingly altered in either salt or Pi signaling pathways in transgenic Arabidopsis plants. CONCLUSIONS: Our work identifies some PHO1 genes as promising genetic materials for soybean improvement, and suggests that expression variation is decisive to functional divergence of the orthologous Gm-GsPHO1 pairs, which plays an adaptive role during soybean evolution.


Assuntos
Proteínas de Transporte de Fosfato/fisiologia , Proteínas de Plantas/fisiologia , Soja/genética , Adaptação Fisiológica , Arabidopsis/genética , Evolução Molecular , Proteínas de Transporte de Fosfato/genética , Proteínas de Transporte de Fosfato/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Estresse Salino/genética , Transdução de Sinais/genética , Soja/metabolismo
6.
Mol Biol (Mosk) ; 53(4): 561-573, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397432

RESUMO

The protein synthesis in cells occurs in ribosomes, with the involvement of protein translational factors. One of these translational factors is the elongation factor P (EF-P). EF-P is a three-domain protein that binds between the P and E sites of the ribosome, near the P-tRNA, the peptidyl transferase center, and E-site codon of the mRNA. The majority of studies showed that the EF-P helps the ribosome to synthesize stalling amino acid motifs, such as polyprolines. In the first part of this review, we inspect the general evolutionary variety of the EF-P in different organisms, the problems of the regulation provided by the EF-P, and its role in the sustainability of the protein balance in the cell in different physiological states. Although the functions of the EF-P have been well studied, there are still some problems that remain to be solved. The data from recent studies contradict the previous theories. Consequently, in the second part, we discuss the recent data that suggest the involvement of the EF-P in each translocation event, not only in those related to poly-proline synthesis. This activity contradicts some aspects of the known pathway of the removal of the E-tRNA during the translocation event. In addition, in the third part of this review, we tried to partly shift the interest from the antistalling activity of domain I of the EF-P to the action of domain III, the functions of which has not been closely studied. We expand on the idea about the involvement of domain III of the EF-P in preventing the frameshift and debate the EF-P's evolutionary history.


Assuntos
Evolução Molecular , Fatores de Alongamento de Peptídeos/metabolismo , Biossíntese de Proteínas , Animais , Humanos , Fatores de Alongamento de Peptídeos/química , RNA de Transferência/genética , RNA de Transferência/metabolismo , Ribossomos/química , Ribossomos/metabolismo
7.
Mol Biol (Mosk) ; 53(4): 600-612, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397434

RESUMO

A new plasmid, pSM22, was isolated from Serratia marcescens and sequenced. Its 43 190-bp sequence with an average GC-content of 58% contains 31 open reading frames (ORFs) which form replication, conjugation, stability, and adaptive modules. The replication module includes a site of initiation of leading-strand synthesis in plasmid replication, a replication termination site (terC), the rep A (=repA1) and repA4 genes, and the copA sequence, which codes for an antisense RNA (asRNA). These structures are functionally integrated in an FII replicon (incompatibility group IncFII). Based on the significant differences between the FII replicon and the canonical sequences of the R plasmids R1 and NR1 (=R100=R222), pSM22 was assigned to a new subtype. The conjugation module includes 13 genes with a high identity to the genes responsible for conjugation of the F plasmid. A comparative genomic analysis showed that the conjugation modules of pSM22 and F are structurally similar. By the conjugation system and the presence of three conserved motifs in relaxase (TraI), pSM22 belongs to the F12 clade of the MOBF type. The stability module includes the resD and parA genes, which are responsible for the resolution of multimeric plasmid forms and their subsequent segregation between daughter cells. The adaptive module contains the microcin H47 (MccH47) secretion/processing and UV resistance genes. The mosaic structure of pSM22 and reductive evolution of its modules suggest high genomic plasticity for the genus Serratia. An analysis of the architecture of the pSM22 modules clarifies the evolutionary relationships among IncF/MOBF12 group plasmids in bacteria of the family Enterobacteriaceae and opens a novel avenue for further comparative genomic studies of Serratia plasmids.


Assuntos
Evolução Molecular , Genômica , Plasmídeos/classificação , Plasmídeos/genética , Replicação do DNA , Genes Bacterianos , Genoma Bacteriano/genética , Replicon/genética , Serratia marcescens/genética
8.
An Acad Bras Cienc ; 91(suppl 3): e20190339, 2019 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-31460595

RESUMO

Genetic drift is the fortuitous occurrence of genetic events that when they become fixed modify the genome of populations. They can take the form of mutations of single nucleotides (SNPs), the insertion or deletion of short sequences (Indels) or the repetitions of short sequences (CNV i.e. copy number variants) or long insertions or deletion (structural modifications). Their frequency is 10-9 to 10-8 depending on the species, or 50 to 100 per birth in humans. The incidence of these de novo mutations is higher when the father is old at conception. It thus appears that genetic drift, which constitutes the initial element of evolution, has a very strong dynamics. Its intervention in the appearance or disappearance of some major phenotypes is complicated by the uncertainties about the genetic mechanisms in heritability which, paradoxically, are only partially understood.


Assuntos
Evolução Molecular , Deriva Genética , Mutação INDEL/genética , Mamíferos/genética , Animais , Humanos , Camundongos , Ratos
9.
Gene ; 718: 144048, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31421189

RESUMO

Main conclusion Among 247 RsAP2/ERF identified, the majority of the 21 representatives were preferably expressed under drought and heat while suppressed under heavy metals, indicating their potential roles in abiotic stress responses and tolerance. APETALA2/Ethylene-Responsive factor (AP2/ERF) transcription factor (TF) is one of the largest gene families in plants that play a fundamental role in growth and development as well as biotic and/or abiotic stresses responses. Although AP2/ERFs have been extensively characterized in many plant species, little is known about this family in radish, which is an important root vegetable with various medicinal properties. The available genome provides valuable opportunity to identify and characterize the global information on AP2/ERF TFs in radish. In this study, a total of 247 ERF family genes were identified from the radish genome, and sequence alignment and phylogenetic analyses classified the AP2/ERF superfamily into five groups (AP2, ERF, DREB, RAV and soloist). Motif analysis showed that other than AP2/ERF domains, other conserved regions were selectively distributed among different clades in the phylogenetic tree. Chromosome location analysis showed that tandem duplication may result in the expansion of RsAP2/ERF gene family. The RT-qPCR analysis confirmed that a proportion of AP2/ERF genes were preferably expressed under drought and heat stresses, whereas they were suppressed under the ABA and heavy metal stresses. These results provided valuable information for further evolutionary and functional characterization of RsAP2/ERF genes, and contributed to genetic improvement of stress tolerances in radish and other root vegetable crops.


Assuntos
Evolução Molecular , Proteínas de Homeodomínio , Metais Pesados/toxicidade , Família Multigênica , Proteínas Nucleares , Filogenia , Proteínas de Plantas , Raphanus , Estresse Fisiológico/efeitos dos fármacos , Estudo de Associação Genômica Ampla , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raphanus/genética , Raphanus/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
10.
Gene ; 720: 144026, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31377315

RESUMO

Mitogenomes in plants are well-known as exhibiting high diversity in genome size architecture and repetitive DNA sequences. In this research study, we report on the complete mitochondrial genomes of S. tuberosa and S. mombin using Illumina paired-end and mate-pair end reads. These genomes were obtained by a combination of methods of de novo assembly and contig extension. The mitogenomes of S. tuberosa and S. mombin showed 779,106 bp and 685,788 bp in length, with a total of 35 genes. Genome comparisons showed many rearrangements that were mediated by repetitive DNA, and also high incorporation of DNA from chloroplast. In summary, we demonstrate: (1) first complete mitochondrial genomes for the genus Spondias; (2) the synteny between S. tuberosa and S. mombin showed rearrangements, mediated by repetitive DNA; (3) that gene content in Spondias mitogenomes is highly conserved; and (4) the high incorporation DNA from chloroplast genome, (5) the mitogenome size is due intergenic spacers and (6) the non-tandem repeats contributes for giant intergenic spacers.


Assuntos
Anacardiaceae/classificação , Anacardiaceae/genética , DNA Mitocondrial/genética , Evolução Molecular , Genoma Mitocondrial , Sequências Repetitivas de Ácido Nucleico
11.
BMC Bioinformatics ; 20(1): 420, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409290

RESUMO

BACKGROUND: Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a relatively homogeneous rate. However, this algorithm had two major shortcomings: (i) it was automated and published as a set of bash scripts, and hence was Linux-specific, and not user friendly, and (ii) it could result in very stringent sequence subselection when extremely slow-evolving sequences were present. RESULTS: We address these challenges and produce a new, platform-independent program, LSX, written in R, which includes a reprogrammed version of the original LS3 algorithm and has added features to make better lineage rate calculations. In addition, we developed and included an alternative version of the algorithm, LS4, which reduces lineage rate heterogeneity by detecting sequences that evolve too fast and sequences that evolve too slow, resulting in less stringent data subselection when extremely slow-evolving sequences are present. The efficiency of LSX and of LS4 with datasets with extremely slow-evolving sequences is demonstrated with simulated data, and by the resolution of a contentious node in the catfish phylogeny that was affected by an unusually high lineage rate heterogeneity in the dataset. CONCLUSIONS: LSX is a new bioinformatic tool, with an accessible code, and with which the effect of lineage rate heterogeneity can be explored in gene sequence datasets of virtually any size. In addition, the two modalities of the sequence subsampling algorithm included, LS3 and LS4, allow the user to optimize the amount of non-phylogenetic signal removed while keeping a maximum of phylogenetic signal.


Assuntos
Evolução Biológica , Evolução Molecular , Software , Algoritmos , Biologia Computacional/métodos , Filogenia
12.
BMC Plant Biol ; 19(1): 290, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266465

RESUMO

BACKGROUND: Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera. RESULTS: All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability. CONCLUSIONS: Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.


Assuntos
Genomas de Plastídeos , Filogenia , Saussurea/genética , Evolução Molecular
13.
BMC Plant Biol ; 19(1): 293, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31272375

RESUMO

BACKGROUND: Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P. japonica remains poorly understood. RESULTS: We used next-generation sequencing to generate complete plastomes of P. japonica, P. verticillata, Trillium govanianum, Ypsilandra thibetica and Y. yunnanensis. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in Paris were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant Paris and Trillium occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between P. japonica and the section Euthyra was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia. CONCLUSIONS: The genome size expansion in the most recent common ancestor for Paris and Trillium was most possibly a gradual process that lasted for approximately 20 million years. The divergence of P. japonica (section Kinugasa) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in P. japonica. Moreover, our results support the taxonomic treatment of Paris as a genus rather than dividing it into three genera, but do not support the recognition of T. govanianum as the separate genus Trillidium.


Assuntos
Tamanho do Genoma , Genoma de Cloroplastos , Genoma de Planta , Melanthiaceae/genética , Cloroplastos , Evolução Molecular , Filogenia
14.
BMC Bioinformatics ; 20(Suppl 14): 335, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31266447

RESUMO

BACKGROUND: Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have been developed to predict changes in the Gibbs free energy of unfolding (∆∆G) between wild type and variant proteins, using sequence and structure information. Most of the available methods however do not exhibit the anti-symmetric prediction property, which guarantees that the predicted ∆∆G value for a variation is the exact opposite of that predicted for the reverse variation, i.e., ∆∆G(A → B) = -∆∆G(B → A), where A and B are amino acids. RESULTS: Here we introduce simple anti-symmetric features, based on evolutionary information, which are combined to define an untrained method, DDGun (DDG untrained). DDGun is a simple approach based on evolutionary information that predicts the ∆∆G for single and multiple variations from sequence and structure information (DDGun3D). Our method achieves remarkable performance without any training on the experimental datasets, reaching Pearson correlation coefficients between predicted and measured ∆∆G values of ~ 0.5 and ~ 0.4 for single and multiple site variations, respectively. Surprisingly, DDGun performances are comparable with those of state of the art methods. DDGun also naturally predicts multiple site variations, thereby defining a benchmark method for both single site and multiple site predictors. DDGun is anti-symmetric by construction predicting the value of the ∆∆G of a reciprocal variation as almost equal (depending on the sequence profile) to -∆∆G of the direct variation. This is a valuable property that is missing in the majority of the methods. CONCLUSIONS: Evolutionary information alone combined in an untrained method can achieve remarkably high performances in the prediction of ∆∆G upon protein mutation. Non-trained approaches like DDGun represent a valid benchmark both for scoring the predictive power of the individual features and for assessing the learning capability of supervised methods.


Assuntos
Algoritmos , Estabilidade Proteica , Proteínas/química , Sequência de Aminoácidos , Evolução Molecular , Humanos , Mutação Puntual , Proteínas/genética , Termodinâmica
15.
DNA Cell Biol ; 38(8): 824-839, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31295023

RESUMO

Tea plant is an important economic crop on a global scale. Its yield and quality are affected by abiotic stress. The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) family genes play irreplaceable roles in plant development and stress resistance. More and more CBL-CIPK genes have been identified, but a few CBL-CIPK genes have been cloned and characterized in tea plants. In this study, 7 CsCBLs and 18 CsCIPKs were identified based on the tea plant genome. Physicochemical properties, phylogenetic, conserved motifs, gene structure, homologous gene network, and promoter upstream elements of these 25 genes were analyzed. Conserved motifs of these genes varied with phylogenetic tree node. From the genetic structure, members of the tea plant CIPK gene family can be divided into two types: intron rich and no intron. Many stress-related elements were found in the 2000 bp upstream of the promoter, and PlantCARE predicted that CsCBL4 contained 30 stress-related elements. PlantPAN2 shows that CsCIPK6 contains 48 ABRELATERD1; CsCIPK17 contains 37 GT1CONSENSUS; CsCIPK3 contains 64 MYBCOREATCYCB1; CsCBL3 contains 52 SORLIP1AT; CsCBL5 contains 65 SURECOREATSULTR11; and CsCIPK11 contains 83 WBOXATNPR1. In addition, eight genes were selected for quantitative real-time PCR (RT-qPCR) to detect their expression profiles under high-temperature, low-temperature, salt, and drought treatments. These genes were found to be responsive to one or more abiotic stress treatments. The expression levels of CsCBL4, CsCIPK2, and CsCIPK14 were similar, and they were homologous to AtSOS3 and AtSIP3 and AtSIP4 in Arabidopsis, which were involved in the SOS pathway. This study provides insight into the potential functions of the CsCBL and CsCIPK of tea plant.


Assuntos
Camellia sinensis/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas Serina-Treonina Quinases/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Arabidopsis/genética , Proteínas de Ligação ao Cálcio/genética , Camellia sinensis/fisiologia , Sequência Conservada , Secas , Evolução Molecular , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética
16.
Genome Biol ; 20(1): 140, 2019 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-31307522

RESUMO

BACKGROUND: Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations (deMs) in enhancer sequences. Here, we focus on elucidating the mechanism underlying the different densities of deMs in human enhancers. RESULTS: We identify two classes of enhancers based on the density of nucleotides prone to deMs. Firstly, fragile enhancers with abundant deM nucleotides are associated with the immune system and regular cellular maintenance. Secondly, stable enhancers with only a few deM nucleotides are associated with the development and regulation of TFs and are evolutionarily conserved. These two classes of enhancers feature different regulatory programs: the binding sites of pioneer TFs of FOX family are specifically enriched in stable enhancers, while tissue-specific TFs are enriched in fragile enhancers. Moreover, stable enhancers are more tolerant of deMs due to their dominant employment of homotypic TF binding site (TFBS) clusters, as opposed to the larger-extent usage of heterotypic TFBS clusters in fragile enhancers. Notably, the sequence environment and chromatin context of the cognate motif, other than the motif itself, contribute more to the susceptibility to deMs of TF binding. CONCLUSIONS: This dichotomy of enhancer activity is conserved across different tissues, has a specific footprint in epigenetic profiles, and argues for a bimodal evolution of gene regulatory programs in vertebrates. Specifically encoded stable enhancers are evolutionarily conserved and associated with development, while differently encoded fragile enhancers are associated with the adaptation of species.


Assuntos
Adaptação Biológica , Elementos Facilitadores Genéticos , Evolução Molecular , Mutação , Animais , Genes Reporter , Células Hep G2 , Humanos , Camundongos Transgênicos
17.
Gene ; 717: 143987, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31362037

RESUMO

To improve the accuracy and genetic progress of blue fox breeding, the relationships between genetic polymorphisms and growth and reproductive traits of the blue fox were investigated. MC4R, MC3R, INHA and INHBA were selected as candidate genes for molecular evolution and statistical analyses. Single-factor variance analyses showed that the MC4R (g.267C > T, g.423C > T, and g.731C > A) and MC3R (g.677C > T) genotypes had significant impacts on body weight, chest circumference, abdominal perimeter and body mass index (BMI) (P < 0.05) in blue fox. The MC4R and MC3R combined genotypes had significant effects on the body weight and abdominal circumference. The different genotypes of INHA g.75G > A had significant effects on female fecundity, whereas the different genotypes of INHBA g.404G > T and g.467G > T and the INHA and INHBA combined genotypes had significant effects on male fecundity. The proteins encoded by the open reading frames (ORFs) of different polymorphic loci were predicted and analysed. The aims of this study were to identify genetic markers related to growth and reproduction in the blue fox and to provide an efficient, economical and accurate theoretical approach for auxiliary fox breeding.


Assuntos
Raposas/crescimento & desenvolvimento , Raposas/genética , Polimorfismo de Nucleotídeo Único , Reprodução/genética , Animais , Tamanho Corporal/genética , Peso Corporal/genética , China , Evolução Molecular , Feminino , Raposas/fisiologia , Marcadores Genéticos , Subunidades beta de Inibinas/química , Subunidades beta de Inibinas/genética , Inibinas/química , Inibinas/genética , Desequilíbrio de Ligação , Masculino , Mutação , Receptor Tipo 3 de Melanocortina/química , Receptor Tipo 3 de Melanocortina/genética , Receptor Tipo 4 de Melanocortina/química , Receptor Tipo 4 de Melanocortina/genética
18.
Naturwissenschaften ; 106(7-8): 44, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31267209

RESUMO

Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations in anticodons, and first and second codon positions in mitogenes. Here we describe deamination gradients across theoretical minimal RNA rings, 22 nucleotide-long RNAs designed to simulate prebiotic RNAs. These RNA rings code for a start/stop codon and a single codon for each amino acid, and form stem-loop hairpins slowing degradation. They resemble consensus tRNAs, defining potential anticodons and cognate amino acids. Theoretical minimal RNA rings are not designed to include deamination gradients, yet deamination gradients occur in RNA rings. tRNA homology produces stronger evidence for deamination gradients than RNA ring homology defined by coding properties. Deamination gradients start at predicted RNA ring anticodons, corresponding to known homologies between mitochondrial tRNAs and replication origins, and between bacterial tRNA synthetases and mitochondrial DNA polymerase gamma. Deamination gradients are strongest for RNA rings with predicted anticodons matching cognate amino acids that integrated early the genetic code. Presumably protections against deaminations evolved while amino acids integrated the genetic code. Results confirm tRNA-RNA ring homologies. Coding constraints defining RNA rings presumably produce deamination gradients starting at predicted anticodons. Hence, the universal genetic code determines nucleotide deamination gradients in theoretical minimal RNA rings, suggesting adaptation to prevent consequences of deamination mutations. Results also indicate that the genetic code's structure determined evolution of tRNAs, their cognates, tRNA synthetases, and polymerases.


Assuntos
Evolução Molecular , Modelos Químicos , RNA/química , Códon/química , Simulação por Computador , Desaminação , RNA de Transferência/química
19.
Cytogenet Genome Res ; 158(3): 152-159, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31272100

RESUMO

Among birds, species with the ZZ/ZW sex determination system generally show significant differences in morphology and size between the Z and W chromosomes (with the W usually being smaller than the Z). In the present study, we report for the first time the karyotype of the spot-flanked gallinule (Gallinula melanops) by means of classical and molecular cytogenetics. The spot-flanked gallinule has 2n = 80 (11 pairs of macrochromosomes and 29 pairs of microchromosomes) with an unusual W chromosome that is larger than the Z. Besides being totally heterochromatic, it has a secondary constriction in its long arm corresponding to the nucleolar organizer region, as confirmed by both silver staining and mapping of 18S rDNA probes. This is an unprecedented fact among birds. Additionally, 18S rDNA sites were also observed in 6 microchromosomes, while 5S rDNA was found in just 1 microchromosomal pair. Seven out of the 11 used microsatellite sequences were found to be accumulated in microchromosomes, and 6 microsatellite sequences were found in the W chromosome. In addition to the involvement of heterochromatin and repetitive DNAs in the differentiation of the large W chromosome, the results also show an alternative scenario that highlights the plasticity that shapes the evolutionary history of bird sex chromosomes.


Assuntos
Aves/genética , Evolução Molecular , Sequências Repetitivas de Ácido Nucleico/genética , Cromossomos Sexuais/genética , Animais , Bandeamento Cromossômico , Mapeamento Cromossômico , Feminino , Cariótipo , Repetições de Microssatélites/genética , Região Organizadora do Nucléolo/genética
20.
Gene ; 713: 143975, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31302167

RESUMO

Hair is one of the defining characteristics of mammals. The hair shaft has a two-layer structure comprising the cortex, which is the inner layer and is composed of cortical cells, and the cuticle, which is the outermost layer. S100 calcium-binding protein A3 (S100A3) is expressed at high levels in the human hair cuticle. Arginine 51 of S100A3 protein is citrullinated specifically by peptidylarginine deiminase 3 (PAD3), and this citrullination is related to maturation of the cuticle. However, the detailed evolutionary processes of S100A3 and PAD3 during mammalian evolution are unknown. Here, we show that nonsynonymous changes in S100A3 accelerated in the common ancestral branch of mammals, probably as a result of positive selection that returned after the acquisition of hair cuticle-specific function in mammals. Later, pseudogenisation or nonfunctionalisation of S100A3 and PAD3 occurred in some species, such as the cetaceans. Our results show that positive selection and relaxation of the functional constraints of genes played important roles in the evolution of mammalian hair.


Assuntos
Evolução Molecular , Cabelo/química , Mamíferos/genética , Desiminases de Arginina em Proteínas/genética , Proteínas S100/genética , Seleção Genética , Sequência de Aminoácidos , Animais , Filogenia , Homologia de Sequência
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