RESUMO
Schisandra chinensis, which has a high development value, has long been used as medicine. Its mature fruits (called Wuweizi in Chinese) have long been used in the famous traditional Chinese medicine (TCM) recorded in the "Chinese Pharmacopoeia." Chloroplasts (CP) are the highly conserved primitive organelles in plants, which can serve as the foundation for plant classification and identification. This study introduced the structures of the CP genomes of three Schisandraceae species and analyzed their phylogenetic relationships. Comparative analyses on the three complete chloroplast genomes can provide us with useful knowledge to identify the three plants. In this study, approximately 5 g fresh leaves were harvested for chloroplast DNA isolation according to the improved extraction method. A total of three chloroplast DNAs were extracted. Afterwards, the chloroplast genomes were reconstructed using denovo combined with reference-guided assemblies. General characteristics of the chloroplast genome and genome comparison with three Schisandraceae species was analyzed by corresponding software. The total sizes of complete chloroplast genomes of S. chinensis, S. sphenanthera, and Kadsura coccinea were 146875 bp, 146842 bp, and 145399 bp, respectively. Altogether, 124 genes were annotated, including 82 protein-coding genes, 34 tRNAs, and 8 rRNAs of all 3 species. In SSR analysis, only S. chinensis was annotated to hexanucleotides. Moreover, comparative analysis of chloroplast Schisandraceae genome sequences revealed that the gene order and gene content were slightly different among Schisandraceae species. Finally, phylogenetic trees were reconstructed, based on the genome-wide SNPs of 38 species. The method can be used to identify and differentially analyze Schisandraceae plants and offer useful information for phylogenetics as well as further studies on traditional medicinal plants.
Assuntos
Cloroplastos/genética , Genoma de Cloroplastos/genética , Plantas Medicinais/genética , Schisandraceae/genética , DNA de Cloroplastos/genética , Ordem dos Genes/genética , Genômica/métodos , Filogenia , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Abscisic acid (ABA) signaling is a vital plant signaling pathway for plant responses to stress conditions. ABA treatment can alter global gene expression patterns and cause significant phenotypic changes. We investigated the responses to ABA treatment during flowering in Arabidopsis thaliana. Dipping the flowers of CARK3 T-DNA mutants in ABA solution, led to less reduction of pollen fertility than in the wild type plants (Col-0). We demonstrated that PMEIL, a gene located downstream of CARK3, directly affects pollen fertility. Due to the close arrangement of CARK3 and PMEIL, CARK3 expression represses transcription of PMEIL in an ABA-dependent manner through transcriptional interference. Our study uncovers a molecular mechanism underlying ABA-mediated pollen sterility and provides an example of how transcriptional interference caused by close arrangement of genes may mediate stress responses during plant reproduction.
Assuntos
Ácido Abscísico/metabolismo , Proteínas de Arabidopsis/genética , Arabidopsis/genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Reguladores de Crescimento de Plantas/fisiologia , Infertilidade das Plantas/genética , Pólen/genética , Proteínas Serina-Treonina Quinases/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/fisiologia , Ordem dos Genes/genética , Ordem dos Genes/fisiologia , Germinação , Peptídeos e Proteínas de Sinalização Intracelular/fisiologia , Reguladores de Crescimento de Plantas/metabolismo , Infertilidade das Plantas/fisiologia , Pólen/fisiologia , Proteínas Serina-Treonina Quinases/fisiologiaRESUMO
The complete mitochondrial genome (mitogenome) of the red-banded lobster, Metanephrops thomsoni (Decapoda, Astacidea, Nephropidae), is 19,835 bp in length and contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 24 transfer RNAs (including additional copies of trnW and trnL1), and 2 control regions (CR). The mitogenome of M. thomsoni has 10 long intergenic sequences (71-237 bp) with a high AT content (70.0%). The two CRs show 59.6% similarity and have an identical sequence region with a length of 295 bp. The mitogenome of M. thomsoni shows a novel gene arrangement compared with the pancrustacean ground pattern and is identical to that of M. sibogae, except for the two additional tRNAs (trnW and trnL1). Phylogenetic tree from maximum likelihood analysis using the concatenated sequences of 13 PCGs depicted M. thomsoni as one of the members of the superfamily Nephropoidea within Astacidea.
Assuntos
Crustáceos/genética , Genoma Mitocondrial/genética , Nephropidae/genética , Animais , Crustáceos/classificação , DNA Mitocondrial/genética , Ordem dos Genes/genética , Nephropidae/classificação , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética , Análise de Sequência de DNARESUMO
The complete chloroplast genome of Morinda officinalis, an endangered and important Chinese medicine with great economic value, has been sequenced in this article. The genome size is 153 398 bp in length, with 38.05% GC content. A pair of inverted repeats (IRs, 51 834 bp) are separated by a large single copy region (LSC, 83 996 bp) and a small single copy region (SSC, 17 566 bp). The chloroplast genome contains 103 unique genes, 80 protein-coding genes, 19 tRNA genes, and 4 rRNA genes. In these genes, 8 genes contained 1 intron, and 2 genes comprised of 2 introns.
Assuntos
Cloroplastos/genética , DNA de Cloroplastos/genética , Morinda/genética , Composição de Bases/genética , Sequência de Bases/genética , China , Sequência Conservada/genética , Ordem dos Genes/genética , Genes de Plantas/genética , Genoma Mitocondrial/genética , Genoma de Planta/genética , Filogenia , Plantas Medicinais/genética , Rubiaceae/genética , Análise de Sequência de DNA/métodosRESUMO
The complete chloroplast sequence of Dendrobium officinale, an endangered and economically important traditional Chinese medicine, was reported and characterized. The genome size is 152,018 bp, with 37.5% GC content. A pair of inverted repeats (IRs) of 26,284 bp are separated by a large single-copy region (LSC, 84,944 bp) and a small single-copy region (SSC, 14,506 bp). The complete cp DNA contains 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Fourteen genes contained one or two introns.
Assuntos
Cloroplastos/genética , DNA de Cloroplastos/genética , Dendrobium/genética , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Composição de Bases/genética , Sequência de Bases , China , Mapeamento Cromossômico , Ordem dos Genes/genética , Genes de Plantas/genética , Tamanho do Genoma/genética , Sequências Repetidas Invertidas/genética , Medicina Tradicional Chinesa , Folhas de Planta/genética , RNA Ribossômico/genética , RNA de Transferência/genética , Análise de Sequência de DNARESUMO
Dioscorea zingiberensis (Dioscoreceae) is an important medicinal plant endemic to China. Here, its chloroplast genome sequence is reconstructed from the whole-genome Illumina sequencing data. The circular genome is 153,970 bp in length, and comprises a pair of inverted repeat (IR) regions of 25,491 bp each, a large single-copy (LSC) region of 83,950 bp and a small single-copy (SSC) region of 19,038 bp. The chloroplast genome contains 132 genes, including 86 protein-coding genes (79 PCG species), 8 ribosomal RNA genes (four rRNA species) and 38 transfer RNA genes (30 tRNA species). Out of these genes, 10 harbor a single intron, and 7 contain a couple of introns. The overall A + T content of the whole genome is 62.8%, while the corresponding values of the LSC, SSC and IR regions are 64.9%, 68.8% and 57.0%, respectively.
Assuntos
Dioscorea/genética , Genoma de Cloroplastos/genética , DNA de Cloroplastos/genética , Dioscorea/classificação , Ordem dos Genes/genética , Genoma de Planta/genética , Íntrons/genética , Filogenia , RNA de Transferência/genética , Análise de Sequência de DNARESUMO
We sequenced 16,971 bp of the linear mitochondrial DNA of the moon jellyfish Aurelia sp. nov. and characterized it by comparing with Aurelia aurita. They had 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with three tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met). Both have another two PCGs, orf969 and orf324 with telomeres at both ends. After comparison of Aurelia sp. nov. with Aurelia aurita, we found low-protein similarity of orf969 (59%) and orf324 (75%), respectively, while the other 13 PCGs showed 80% to 98% protein similarities.
Assuntos
Genoma Mitocondrial/genética , Cifozoários/genética , Animais , Composição de Bases/genética , Sequência de Bases , Códon/genética , Ordem dos Genes/genética , Dados de Sequência Molecular , República da Coreia , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
We sequenced 16,775 bp of the linear mitochondrial DNA of the jellyfish Chrysaora quinquecirrha and characterized them. C. quinquecirrha has 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with 3 tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met) as shown in Aurelia sp. nov. Both have another two PCGs such as helicase and orf363 with telomeres at both ends. The PCGs of C. quinquecirrha shows anti-G bias on 2nd and 3rd positions of PCGs as well as anti-C bias on 1st and 3rd positions of PCGs.
Assuntos
Genoma Mitocondrial/genética , Cifozoários/genética , Animais , Composição de Bases/genética , Sequência de Bases , Códon/genética , Ordem dos Genes/genética , Dados de Sequência Molecular , República da Coreia , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.
Assuntos
Cnidários/genética , DNA Mitocondrial/genética , Evolução Molecular , Genoma Mitocondrial/genética , Animais , Sequência de Bases , Linhagem da Célula/genética , Cubomedusas/genética , Fragmentação do DNA , Replicação do DNA/genética , DNA Polimerase Dirigida por DNA/genética , Ordem dos Genes/genética , Hidrozoários/genética , Mitocôndrias/genética , Anotação de Sequência Molecular/métodos , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Fases de Leitura Aberta/genética , Filogenia , Recombinação Genética/genética , Cifozoários/genética , Transcrição Gênica/genéticaRESUMO
Glucose, a carbohydrate metabolite, plays a major role in the energy supply for fish iono- and osmoregulation, and the way that glucose is transported in ionocytes is a critical process related to the functional operations of ionocytes. Eighteen members of glucose transporters (GLUTs, SLC2A) were cloned and identified from zebrafish. Previously, Na(+),K(+)-ATPase-rich (NaR), Na(+)-Cl(-) cotransporter-expressing (NCC), H(+)-ATPase-rich (HR), and glycogen-rich (GR) cells have been identified to be responsible for Ca(2+) uptake, Cl(-) uptake, Na(+) uptake, and the energy deposition, respectively, in zebrafish skin/gills. The purpose of the present study was to test the hypothesis of whether GLUT isoforms are specifically expressed and function in ionocytes to supply energy for ion regulatory mechanisms. On the basis of translational knockdown of foxi3a/3b (2 transcriptional factors related to the ionocytes' differentiation) and triple in situ hybridization/immunocytochemistry, 3 GLUT isoforms, zglut1a, -6, and -13.1, were specifically localized in NaR/NCC cells, GR cells, and HR cells, respectively. mRNA expression of zglut1a in embryos and adult gills were stimulated by the low Ca(2+) or low Cl(-) freshwater, which has been previously reported to upregulate the functions (monitored by epithelial Ca(2+) channel, NCC mRNA) of NaR/NCC cells, respectively while that of zglut13.1 was stimulated only by low Na(+), a situation to upregulate the function (monitored by carbonic anhydrase 15a mRNA) of HR cells. On the other hand, ambient ion compositions did not affect the zglut6 mRNA expression. Taken together, zGLUT1a, -6, and 13.1, the specific transporters in NaR/NCC cells, GR cells, and HR cells, may absorb glucose into the respective cells to fulfill different physiological demands.
Assuntos
Células Epiteliais/metabolismo , Regulação da Expressão Gênica , Brânquias/citologia , Proteínas Facilitadoras de Transporte de Glucose/metabolismo , Proteínas de Peixe-Zebra/metabolismo , Peixe-Zebra/metabolismo , Aclimatação/genética , Sequência de Aminoácidos , Estruturas Animais/metabolismo , Animais , Cálcio/farmacologia , Cloretos/farmacologia , Clonagem Molecular , DNA Complementar/genética , Fatores de Transcrição Forkhead/genética , Expressão Gênica/efeitos dos fármacos , Expressão Gênica/genética , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Ordem dos Genes/genética , Brânquias/metabolismo , Proteínas Facilitadoras de Transporte de Glucose/química , Proteínas Facilitadoras de Transporte de Glucose/genética , Larva/metabolismo , Proteínas de Membrana/química , Dados de Sequência Molecular , Oligonucleotídeos Antissenso/genética , Filogenia , Isoformas de Proteínas/genética , Estrutura Terciária de Proteína/genética , Homologia de Sequência de Aminoácidos , Pele/metabolismo , Sódio/farmacologia , Peixe-Zebra/genética , Proteínas de Peixe-Zebra/química , Proteínas de Peixe-Zebra/genéticaRESUMO
Hepcidin is an antimicrobial peptide and putative iron regulatory hormone previously described in mice and humans. Dozens of fish hepcidins have been isolated and characterized so far. Here we present seven hepcidin-like cDNA sequences named AS-hepc1-7, amplified from the normal commercially cultured fish (black porgy) by RACE-PCR. Sequence analysis reveals that these seven potential hepcidin peptides have highly conserved sequences with other known hepcidins, but they are different from each other in constitution and characteristics of predicted mature amino acids. Based on the study, it is deduced that AS-hepc1-7 represent different variants of a family of hepcidin genes in black porgy. To understand the organization of these hepcidin-like genes, we sequenced AS-hepc2 DNA, AS-hepc3 DNA, AS-hepc4 DNA, AS-hepc7 DNA and AS-hepc2 upstream region; and all of the four genomic DNAs consisted of two introns and three exons, the same organization as other reported hepcidins. The tissue-specific gene expression of hepcidins in normal black porgy was evaluated using RT-PCR and dot blot approaches. RT-PCR showed that transcripts of hepcidin-like mRNAs were present in each tested tissue of normal juvenile black porgy, including liver, spleen, kidney, heart, brain, stomach, intestine, gill, skin and blood, but abundant hepcidin-like mRNA transcripts were only detected in the liver, kidney, spleen, intestine and stomach by dot blot assay. In addition, using dot blot and Northern blot approach, a significant increase of hepcidin mRNA transcription was observed in the liver within 48 h after immersion in a suspension of live bacteria, which suggested that the expression pattern of hepcidin-like genes in black porgy might be different in the liver from the other tissues as previously reported in several hepcidin studies.
Assuntos
Peptídeos Catiônicos Antimicrobianos/genética , Regulação da Expressão Gênica , Ordem dos Genes/genética , Perciformes/genética , Perciformes/metabolismo , Sequência de Aminoácidos , Animais , Peptídeos Catiônicos Antimicrobianos/química , Infecções Bacterianas/metabolismo , Infecções Bacterianas/veterinária , Fenômenos Fisiológicos Bacterianos , Sequência de Bases , Clonagem Molecular , DNA Complementar/genética , Doenças dos Peixes/metabolismo , Doenças dos Peixes/microbiologia , Perfilação da Expressão Gênica , Hepcidinas , Dados de Sequência Molecular , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA , Fatores de TempoRESUMO
Plants in the genus Cucumis (cucumber and melon) have the largest mitochondrial genomes known among all plants, due in part to the accumulation of repetitive DNAs of varying complexities. Recombination among these repetitive DNAs should produce highly rearranged mitochondrial genomes relative to the smaller mitochondrial genomes of related plants. We cloned and sequenced mitochondrial genomic regions near the rRNA, atp9 and cob genes from cucumber, melon, squash and watermelon (all members of the Cucurbitaceae family), and compared to the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugar beet to study the distribution and arrangement of coding and repetitive DNAs. Cucumber and melon had regions of concentrated repetitive DNAs spread throughout the sequenced regions; few repetitive DNAs were revealed in the mitochondrial genomes of A. thaliana, sugar beet, squash and watermelon. Recombination among these repetitive DNAs most likely produced unique arrangements of the rrn18 and rrn5 genes in the genus Cucumis. Cucumber mitochondrial DNA had more pockets of dispersed direct and inverted repeats than melon and the other plants, and we did not reveal repetitive sequences significantly contributing to mitochondrial genome expansion in both cucumber and melon.