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Pesquisa : G05.360.340.024.340.385 [Categoria DeCS]
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[PMID]:28786999
[Au] Autor:Sunil M; Hariharan N; Dixit S; Choudhary B; Srinivasan S
[Ad] Endereço:Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India.
[Ti] Título:Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus.
[So] Source:PLoS One;12(8):e0180528, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Genome duplication event in edible dicots under the orders Rosid and Asterid, common during the oligocene period, is missing for species under the order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits missing in species under rosids and asterids. For example, grain amaranths display traits like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection and resilience to stress. It is, therefore, of interest to look for minor genome rearrangements with potential functional implications that are unique to grain amaranths. Here, by deep sequencing and assembly of 16 transcriptomes (86.8 billion bases) we have interrogated differential genome rearrangement unique to Amaranthus hypochondriacus with potential links to these phenotypes. We have predicted 125,581 non-redundant transcripts including 44,529 protein coding transcripts identified based on homology to known proteins and 13,529 predicted as novel/amaranth specific coding transcripts. Of the protein coding de novo assembled transcripts, we have identified 1810 chimeric transcripts. More than 30% and 19% of the gene pairs within the chimeric transcripts are found within the same loci in the genomes of A. hypochondriacus and Beta vulgaris respectively and are considered real positives. Interestingly, one of the chimeric transcripts comprises two important genes, namely DHDPS1, a key enzyme implicated in the biosynthesis of lysine, and alpha-glucosidase, an enzyme involved in sucrose catabolism, in close proximity to each other separated by a distance of 612 bases in the genome of A. hypochondriacus in a convergent configuration. We have experimentally validated that transcripts of these two genes are also overlapping in the 3' UTR with their expression negatively correlated from bud to mature seed, suggesting a potential link between the high seed lysine trait and unique genome organization.
[Mh] Termos MeSH primário: Amaranthus/genética
Amaranthus/metabolismo
Genoma de Planta
Transcriptoma
[Mh] Termos MeSH secundário: Beta vulgaris/genética
Beta vulgaris/metabolismo
Análise por Conglomerados
Biologia Computacional
Fusão Gênica
Homologia de Genes
Loci Gênicos
Sequenciamento de Nucleotídeos em Larga Escala
Lisina/metabolismo
Fenótipo
Proteínas de Plantas/genética
Proteínas de Plantas/metabolismo
Sementes/genética
Sementes/metabolismo
Homologia de Sequência
alfa-Glucosidases/genética
alfa-Glucosidases/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Plant Proteins); EC 3.2.1.20 (alpha-Glucosidases); K3Z4F929H6 (Lysine)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171004
[Lr] Data última revisão:
171004
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170809
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0180528


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[PMID]:28167103
[Au] Autor:Inouye M; Ishida Y; Inouye K
[Ad] Endereço:Department of Biochemistry, Rutgers-Robert Wood Johnson Medical School, Center for Advance Biotechnology and Medicine, Piscataway, NJ 08854, USA. Electronic address: inouye@cabm.rutgers.edu.
[Ti] Título:Designing of a single gene encoding four functional proteins.
[So] Source:J Theor Biol;419:266-268, 2017 Apr 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:In the genomes of some organisms such as bacteriophages and bacteria, a DNA sequence is able to encode two different proteins, indicating that genetic information is compacted in DNA twice denser than in usual DNA. In theory, a DNA sequence has a maximal capacity to produce six different mRNAs, however, it is an intriguing question how many of these mRNAs are able to synthesize functional proteins. Here, we design a DNA sequence encoding four collagen-like proteins, two, (Gly-Arg-Pro)n and (Gly-Ala-Pro)n, from a sense mRNA and the other two, also (Gly-Arg-Pro)n and (Gly-Ala-Pro)n from its antisense mRNA, all of which are expected to form triple-helical structures unique to collagens. Other designs such as the combination of (Gly-Arg-Pro)n, (Gly-Val-Pro)n, (Gly-Thr-Pro)n and (Gly-Arg-Pro)n are also possible. The proposed DNA sequence is considered to contain the most compact genetic information ever created.
[Mh] Termos MeSH primário: DNA/genética
Homologia de Genes/genética
Genes Sintéticos/genética
Proteínas/genética
RNA Mensageiro/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sequência de Bases
Colágeno/genética
DNA Antissenso/genética
Modelos Genéticos
Biossíntese de Proteínas
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Antisense); 0 (Proteins); 0 (RNA, Messenger); 9007-34-5 (Collagen); 9007-49-2 (DNA)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170925
[Lr] Data última revisão:
170925
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170208
[St] Status:MEDLINE


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[PMID]:28061810
[Au] Autor:Taylor LJ; Strebel K
[Ad] Endereço:Viral Biochemistry Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. louist@upenn.edu.
[Ti] Título:Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.
[So] Source:BMC Microbiol;17(1):12, 2017 Jan 07.
[Is] ISSN:1471-2180
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts. RESULTS: Pyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes. CONCLUSIONS: Pyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface ( http://louiejtaylor.github.io/pyViKO/ ), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.
[Mh] Termos MeSH primário: Técnicas de Inativação de Genes/instrumentação
Técnicas de Inativação de Genes/métodos
Homologia de Genes/genética
Vírus/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sequência de Bases
Clonagem Molecular
Códon
Biologia Computacional/métodos
Bases de Dados Genéticas
Genes Virais/genética
Genoma Viral
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Codon)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170925
[Lr] Data última revisão:
170925
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170108
[St] Status:MEDLINE
[do] DOI:10.1186/s12866-016-0920-3


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[PMID]:28035465
[Au] Autor:Zhao H; Nyholt DR
[Ad] Endereço:Statistical and Genomic Epidemiology Laboratory, Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, Brisbane, QLD, 4001, Australia. Huiying.zhao@qut.edu.au.
[Ti] Título:Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders.
[So] Source:Hum Genet;136(2):263-274, 2017 Feb.
[Is] ISSN:1432-1203
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Studies using genome-wide association (GWA) single nucleotide polymorphism (SNP) level data have indicated genetic overlap across the five major disorders in the Psychiatric Genomics Consortium (PGC): attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BPD), major depressive disorder (MDD), and schizophrenia (SCZ). However, such SNP-level analyses reveal little about the underlying biology and are reliant on correlated SNP effects across disorders. In contrast to SNPs, genes are more closely related to biology and gene-based tests can incorporate allelic heterogeneity. This study aimed to extend genetic overlap analysis across the five disorders from SNP level to gene level using a novel gene-based approach. Gene-based tests for association were performed using PGC GWA summary results for the five disorders in samples including 33,332 cases and 27,888 controls of European ancestry. After accounting for non-independence of gene-based test results, we determined whether the proportion of genes with association across multiple disorders was more than expected by chance. Similar to previous SNP-level analyses, we observed significant pairwise genetic overlap between ASD, BPD, MDD and SCZ. However, our approach also produced evidence for genetic overlap between ADHD and ASD, ADHD and BPD, and ADHD and MDD. Combining gene-based association results across disorders, 36 genes produced genome-wide significant P values (<3.2 × 10 ). Pathway analysis of genes with P values <1.0 × 10 highlighted magnesium ion binding and transport, as well as signal peptide processing, and provide insight into the biological mechanisms underlying these major psychiatric disorders.
[Mh] Termos MeSH primário: Alelos
Homologia de Genes
Heterogeneidade Genética
Testes Genéticos
Transtornos Mentais/genética
[Mh] Termos MeSH secundário: Transtorno do Espectro Autista/genética
Transtorno Bipolar/genética
Estudos de Casos e Controles
Transtorno Depressivo Maior/genética
Grupo com Ancestrais do Continente Europeu/genética
Predisposição Genética para Doença
Estudo de Associação Genômica Ampla
Seres Humanos
Modelos Lineares
Polimorfismo de Nucleotídeo Único
Esquizofrenia/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1707
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161231
[St] Status:MEDLINE
[do] DOI:10.1007/s00439-016-1755-6


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[PMID]:27737786
[Au] Autor:Lèbre S; Gascuel O
[Ad] Endereço:IMAG, UMR 5149 - CNRS & Université de Montpellier, France; CPBS, UMR 5236 - CNRS & Université de Montpellier, France; Université Paul Valéry Montpellier 3, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 - CNRS & Université de Montpellier, France. Electronic address: sophie.lebre@umontpellier.fr.
[Ti] Título:The combinatorics of overlapping genes.
[So] Source:J Theor Biol;415:90-101, 2017 Feb 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Overlapping genes exist in all domains of life and are much more abundant than expected upon their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading frames in the sense strand, denoted by +1 and +2, and in three reading frames in the opposite strand, denoted by -0, -1, and -2. This motivated numerous researchers to study the constraints induced by the genetic code on the various overlapping frames, mostly based on information theory. Our focus in this paper is on the constraints induced on two overlapping genes in terms of amino acids, as well as polypeptides. We show that simple linear constraints bind the amino-acid composition of two proteins encoded by overlapping genes. Novel constraints are revealed when polypeptides are considered, and not just single amino acids. For example, in double-coding sequences with an overlapping reading frame -2, each Tyrosine (denoted as Tyr or Y) in the overlapping frame overlaps a Tyrosine in the reference frame +0 (and reciprocally), whereas specific words (e.g. YY) never occur. We thus distinguish between null constraints (YY = 0 in frame -2) and non-null constraints (Y in frame +0 ⇔ Y in frame -2). Our equivalence-based constraints are symmetrical and thus enable the characterization of the joint composition of overlapping proteins. We describe several formal frameworks and a graph algorithm to characterize and compute these constraints. As expected, the degrees of freedom left by these constraints vary drastically among the different overlapping frames. Interestingly, the biological meaning of constraints induced on two overlapping proteins (hydropathy, forbidden di-peptides, expected overlap length …) is also specific to the reading frame. We study the combinatorics of these constraints for overlapping polypeptides of length n, pointing out that, (i) except for frame -2, non-null constraints are deduced from the amino-acid (length = 1) constraints and (ii) null constraints are deduced from the di-peptide (length = 2) constraints. These results yield support for understanding the mechanisms and evolution of overlapping genes, and for developing novel overlapping gene detection methods.
[Mh] Termos MeSH primário: Sequência de Aminoácidos/genética
Homologia de Genes
Fases de Leitura Aberta
Proteínas/genética
[Mh] Termos MeSH secundário: Algoritmos
Animais
Evolução Biológica
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170925
[Lr] Data última revisão:
170925
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161015
[St] Status:MEDLINE


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[PMID]:27578037
[Au] Autor:Xin C; Wu B; Li J; Gong P; Yang J; Li H; Cai X; Zhang X
[Ad] Endereço:College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, China.
[Ti] Título:Complete genome sequence and evolution analysis of Eimeria stiedai RNA virus 1, a novel member of the family Totiviridae.
[So] Source:Arch Virol;161(12):3571-3576, 2016 Dec.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Eimeria stiedai (E. stiedai) is a coccidian that infects the liver of the domestic rabbit and may cause severe hepatic coccidiosis. Virus-like particles in E. stiedai were discovered by Revets et al. However, the complete genome sequence of the E. stiedai virus has yet to be determined. A novel virus was isolated from E. stiedai in the present study. The complete genome sequence of the E. stiedai virus was 6219 bp in length and contained two open reading frames (ORFs) with a tetranucleotide overlap (AUGA). ORF1 (2400 bp) encoded a putative coat protein of 799 amino acids (86.471 kDa) that exhibited a high level of amino acid sequence similarity to that of Eimeria tenella (E. tenella) RNA virus 1 (EtRV1; 43 % identity, NC_026140), whereas ORF2 (3303 bp) encoded a putative RNA-dependent RNA polymerase (RdRp) of 1100 amino acids (118.850 kDa) that exhibited a high level of amino acid sequence similarity to that of the E. tenella RNA virus 1 (EtRV1; 51 % identity, NC_026140). Phylogenetic analysis revealed that the E. stiedai virus was a new member of the family Totiviridae. The sequence data provided sufficient information for classification of eimeriaviruses.
[Mh] Termos MeSH primário: Eimeria/virologia
Genoma Viral
RNA Viral/genética
Análise de Sequência de DNA
Totiviridae/classificação
Totiviridae/genética
[Mh] Termos MeSH secundário: Animais
Proteínas do Capsídeo/genética
Análise por Conglomerados
Coccidiose/parasitologia
Coccidiose/veterinária
Eimeria/isolamento & purificação
Homologia de Genes
Fases de Leitura Aberta
Filogenia
RNA Replicase/genética
Coelhos
Homologia de Sequência de Aminoácidos
Totiviridae/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Capsid Proteins); 0 (RNA, Viral); EC 2.7.7.48 (RNA Replicase)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170126
[Lr] Data última revisão:
170126
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160901
[St] Status:MEDLINE


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[PMID]:27502206
[Au] Autor:Jie S; Li M; Gan M; Zhu J; Yin H; Liu X
[Ad] Endereço:School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
[Ti] Título:Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.
[So] Source:BMC Microbiol;16(1):179, 2016 Aug 08.
[Is] ISSN:1471-2180
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. RESULTS: A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. CONCLUSIONS: This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River.
[Mh] Termos MeSH primário: Sedimentos Geológicos/química
Sedimentos Geológicos/microbiologia
Metais Pesados/análise
Consórcios Microbianos/genética
Rios/química
Rios/microbiologia
Microbiologia da Água
Poluentes Químicos da Água/química
[Mh] Termos MeSH secundário: China
Análise por Conglomerados
Sondas de DNA
Monitoramento Ambiental/métodos
Homologia de Genes
Variação Genética
Mapeamento Geográfico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Probes); 0 (Metals, Heavy); 0 (Water Pollutants, Chemical)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170531
[Lr] Data última revisão:
170531
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160810
[St] Status:MEDLINE
[do] DOI:10.1186/s12866-016-0800-x


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[PMID]:26988143
[Au] Autor:Key FM; Fu Q; Romagné F; Lachmann M; Andrés AM
[Ad] Endereço:Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
[Ti] Título:Human adaptation and population differentiation in the light of ancient genomes.
[So] Source:Nat Commun;7:10775, 2016 Mar 18.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles--especially those associated with pigmentation--are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.
[Mh] Termos MeSH primário: Adaptação Biológica/genética
Genética Populacional
Genoma Humano
[Mh] Termos MeSH secundário: Alelos
Grupo com Ancestrais do Continente Asiático/genética
Grupo com Ancestrais do Continente Europeu/genética
Homologia de Genes
Haplótipos/genética
Seres Humanos
Polimorfismo de Nucleotídeo Único/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1608
[Cu] Atualização por classe:160326
[Lr] Data última revisão:
160326
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160319
[St] Status:MEDLINE
[do] DOI:10.1038/ncomms10775


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[PMID]:26853049
[Au] Autor:Saha D; Podder S; Panda A; Ghosh TC
[Ad] Endereço:Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Electronic address: deeya@jcbose.ac.in.
[Ti] Título:Overlapping genes: A significant genomic correlate of prokaryotic growth rates.
[So] Source:Gene;582(2):143-7, 2016 May 15.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to explore whether OGs act as a potential correlate of prokaryotic growth rates. For this purpose, we compiled a dataset of 25 archaeal and 117 eubacterial genomes and analyzed the inter-correlation between the proportion of overlapping regions in these genomes with their growth rates. Here, we observed that the proportion of overlapping region holds a significant negative correlation with generation time in archaeal domain, whereas no correlation was observed in the eubacterial domain. However, after masking the effect of tRNA, rRNA multiplicity and environmental diversity, OGs show an independent effect over growth rates in the eubacterial domain as well as in the archaeal domain. Moreover, the influence of OGs on prokaryotic growth rates provides different delineations in archaeal and eubacterial domains. In archaea, both long overlap frequency (LOF) and short overlap frequency (SOF) influence the growth rates by increasing the degree of operonization. On the contrary, in the case of bacteria, neither SOF nor LOF plays any significant role in achieving faster growth rates.
[Mh] Termos MeSH primário: Archaea/crescimento & desenvolvimento
Archaea/genética
Bactérias/crescimento & desenvolvimento
Bactérias/genética
Homologia de Genes
Genoma Arqueal
Genoma Bacteriano
[Mh] Termos MeSH secundário: Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1607
[Cu] Atualização por classe:160309
[Lr] Data última revisão:
160309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160209
[St] Status:MEDLINE


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[PMID]:26701149
[Au] Autor:Liu QN; Chai XY; Bian DD; Zhou CL; Tang BP
[Ad] Endereço:Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng
[Ti] Título:The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects.
[So] Source:Genome;59(1):37-49, 2016 Jan.
[Is] ISSN:1480-3321
[Cp] País de publicação:Canada
[La] Idioma:eng
[Ab] Resumo:The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem-loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.
[Mh] Termos MeSH primário: Genes de Insetos
Genoma Mitocondrial
Lepidópteros/genética
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Códon
DNA Intergênico
Homologia de Genes
Região de Controle de Locus Gênico
Filogenia
RNA Ribossômico/genética
RNA de Transferência
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Codon); 0 (DNA, Intergenic); 0 (RNA, Ribosomal); 9014-25-9 (RNA, Transfer)
[Em] Mês de entrada:1606
[Cu] Atualização por classe:161020
[Lr] Data última revisão:
161020
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151225
[St] Status:MEDLINE
[do] DOI:10.1139/gen-2015-0079



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