RESUMEN
BACKGROUND: Artemisia selengensis is traditional Chinese medicine and phytochemical analysis indicated that A. selengensis contains essential oils, fatty acids and phenolic acids. The lack of reference genomic information may lead to tardiness in molecular biology research of A. selengensis. METHOD AND RESULTS: Karyotype analysis, genome survey, and genome assembly was employed to acquire information on the genome structure of A. selengensis. The chromosome number is 2n = 2x = 36, karyotype formula is 28 m + 8Sm, karyotype asymmetry coefficient is 58.8%, and karyotypes were symmetric to Stebbins' type 2A. Besides, the flow cytometry findings reported that the mean peak value of fluorescent intensity is 1,170,677, 2C DNA content is 12 pg and the genome size was estimated to be approximately 5.87 Gb. Furthermore, the genome survey generates 341,478,078 clean reads, unfortunately, after K-mer analysis, no significant peak can be observed, the heterozygosity, repetitive rate and genome size was unable to estimated. It is speculated that this phenomenon might be due to the complexity of genome structure. 37,266 contigs are preliminary assembled with Oxford Nanopore Technology (ONT) sequencing, totaling 804 Mb and GC content was 34.08%. The total length is 804,475,881 bp, N50 is 29,624 bp, and the largest contig length is 239,792 bp. CONCLUSION: This study reveals the preliminary information of genome size of A. selengensis. These findings may provide supportive information for sequencing and assembly of whole-genome sequencing and encourage the progress of functional gene discovery, genetic improvement, evolutionary study, and structural studies of A. selengensis.
Asunto(s)
Artemisia/genética , Composición de Base/genética , Tamaño del Genoma/genética , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Cariotipo , Cariotipificación/métodos , Anotación de Secuencia Molecular/métodos , Filogenia , Análisis de Secuencia de ADN/métodos , Secuenciación Completa del GenomaRESUMEN
Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90 Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07 Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77 Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07 Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.
Asunto(s)
Variación Genética , Repeticiones de Microsatélite/genética , Ranunculales/genética , Composición de Base/genética , Mapeo Cromosómico , Marcadores Genéticos/genética , Genoma de Planta/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Fenotipo , Filogenia , Polimorfismo GenéticoRESUMEN
BACKGROUND: Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. OBJECTIVE: In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. METHODS: Genome sequencing was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). RESULTS: The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. CONCLUSION: In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.
Asunto(s)
Polisacárido Liasas/genética , Sphingomonadaceae/genética , Sphingomonas/genética , Composición de Base/genética , Secuencia de Bases/genética , Mapeo Cromosómico/métodos , Genoma Bacteriano/genética , Genómica/métodos , Pectinas/metabolismo , Filogenia , Sphingomonadaceae/enzimología , Sphingomonadaceae/metabolismo , Sphingomonas/metabolismo , Uganda , Secuenciación Completa del Genoma/métodosRESUMEN
Cancer-related mortality of solid tumors remains the major cause of death worldwide. Circulating tumor DNA (ctDNA) released from cancer cells harbors specific somatic mutations. Sequencing ctDNA opens opportunities to non-invasive population screening and lays foundations for personalized therapy. In this study, two commercially available platforms, Roche's Avenio ctDNA Expanded panel and QIAgen's QIAseq Human Comprehensive Cancer panel were compared for (1) panel coverage of clinically relevant variants; (2) target enrichment specificity and sequencing performance; (3) the sensitivity; (4) concordance and (5) sequencing coverage using the same human blood sample with ultra-deep next-generation sequencing. Our finding suggests that Avenio detected somatic mutations in common cancers in over 70% of patients while QIAseq covered nearly 90% with a higher average number of variants per patient (Avenio: 3; QIAseq: 8 variants per patient). Both panels demonstrated similar on-target rate and percentage of reads mapped. However, Avenio had more uniform sequencing coverage across regions with different GC content. Avenio had a higher sensitivity and concordance compared with QIAseq at the same sequencing depth. This study identifies a unique niche for the application of each of the panel and allows the scientific community to make an informed decision on the technologies to meet research or application needs.
Asunto(s)
ADN Tumoral Circulante/sangre , ADN de Neoplasias/sangre , Composición de Base/genética , Biomarcadores de Tumor/sangre , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , MutaciónRESUMEN
An aerobic bacterium, designated strain Dysh456T, was isolated from a crude oil-contaminated soil. Cells of strain Dysh456T were rod-shaped, motile, and Gram-stain-negative. Strain Dysh456T grew at 13-48 °C and pH 4.3-7.9. Major cellular fatty acids were iso-C15:0 (42.5%), iso-C17:0 (15.3%) and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl [13.7%]). Major respiratory quinone was ubiquinone-8. The genome of strain Dysh456T consists of a single circular chromosome of 2,874,969 bp in length with G + C content of 68.3%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain Dysh456T belongs to the family Rhodanobacteraceae, but none of the existing genera can accommodate this novel isolate. On the basis of physiological, chemotaxonomic, and genomic properties, strain Dysh456T (= NBRC 112897T = DSM 105662T) is proposed as the type strain representing a novel species of novel genus, for which the name Aerosticca soli gen. nov., sp. nov. is proposed.
Asunto(s)
Petróleo/microbiología , Xanthomonadaceae/clasificación , Xanthomonadaceae/aislamiento & purificación , Técnicas de Tipificación Bacteriana , Composición de Base/genética , ADN Bacteriano/genética , Ácidos Grasos/química , Gammaproteobacteria/genética , Fosfolípidos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Suelo , Microbiología del Suelo , Ubiquinona/análisis , Xanthomonadaceae/genéticaRESUMEN
Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production. We sought to obtain hemicellulolytic/cellulolytic bacteria from The Cedars springs that are capable of withstanding the extreme alkaline conditions wherein calcium hydroxide-rich water removes lignin, making cell wall polysaccharides more accessible to microorganisms and their enzymes. We enriched for such bacteria by adding plant debris from the springs into a synthetic alkaline medium with ground tissue of the biofuel crop switchgrass (Panicum virgatum L.) as the sole source of carbon. From the enrichment culture we isolated the facultative anaerobic bacterium Cellulomonas sp. strain FA1 (NBRC 114238), which tolerates high pH and catabolizes the major plant cell wall-associated polysaccharides cellulose, pectin, and hemicellulose. Strain FA1 in monoculture colonized the plant material and degraded switchgrass at a faster rate than the community from which it was derived. Cells of strain FA1 could be acclimated through subculturing to grow at a maximal concentration of 13.4% ethanol. A strain FA1-encoded ß-1, 4-endoxylanase expressed in E. coli was active at a broad pH range, displaying near maximal activity at pH 6-9. Discovery of this bacterium illustrates the value of extreme alkaline springs in the search for microorganisms with potential for consolidated bioprocessing of plant biomass to biofuels and other valuable bio-inspired products.
Asunto(s)
Biocombustibles/microbiología , Cellulomonas/aislamiento & purificación , Cellulomonas/metabolismo , Endo-1,4-beta Xilanasas/metabolismo , Lignina/metabolismo , Composición de Base/genética , Biomasa , Celulosa/metabolismo , Endo-1,4-beta Xilanasas/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Etanol/metabolismo , Panicum/química , Panicum/genética , Panicum/metabolismo , Pectinas/metabolismo , Filogenia , Plantas/metabolismo , Polisacáridos/metabolismo , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Strain YIM PH21724T was isolated from the rhizosphere of Panax notoginseng. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain exhibits close phylogenetic relatedness to Nocardia kroppenstedtii N1286T (97.70%), Nocardia farcinica NCTC 11134T (97.67%) and Nocardia puris DSM 44599T (97.40%). The menaquinones were identified as MK-9 (H4), MK-8 (H4, ω-cyclo) and MK-8 (H4), and the major fatty acids (> 10%) were identified as C16:0, C18:1 ω9c and C18:0 10-methyl. The polar lipids were found to be composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified lipid. The G + C content of the genomic DNA was determined to be 67.01 mol%. The phenotypic, chemotaxonomic, phylogenetic and genomic results clearly show strain YIM PH21724T should be classified in the genus Nocardia and represents a novel species, for which the name Nocardia panacis sp. nov. is proposed. The type strain is YIM PH21724T (= DSM 105904T = KCTC 49030T = CCTCC AA 2017043T).
Asunto(s)
Actinobacteria/efectos de los fármacos , Panax notoginseng/química , Extractos Vegetales/farmacología , Rizosfera , Composición de Base/genética , Composición de Base/fisiología , Cardiolipinas/metabolismo , ADN Bacteriano/metabolismo , Nocardia , Fosfatidiletanolaminas/metabolismo , Fosfatidilinositoles/metabolismo , Filogenia , Extractos Vegetales/química , ARN Ribosómico 16S/metabolismo , Microbiología del Suelo , Vitamina K 2/metabolismoRESUMEN
Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.
Asunto(s)
Alpinia/genética , ADN de Cloroplastos/genética , Genoma del Cloroplasto/genética , Zingiberaceae/genética , Composición de Base/genética , Cloroplastos/genética , Repeticiones de Microsatélite/genética , Estructura Molecular , Filogenia , Secuenciación Completa del Genoma/métodosRESUMEN
A Gram-positive bacterium (DCY118T) was isolated from ginseng-cultivated soil in Gochang-gun, Republic of Korea. This isolate was assigned to the genus Ornithinimicrobium and is closely related to Ornithinimicrobium kibberense K22-20T (98.8%), O. pekingense DSM 21552T (98.5%), O. algicola JC311T (98.2%), and O. humiphilum DSM 12362T (97.9%) based on 16S rRNA gene sequence analysis. However, strain DCY118T showed < 55% DNA-DNA homology with closely related reference strains. Cells were non-motile, non-sporulating, catalase- and oxidase-positive, aerobic, short rods, and cocci, and produced light-yellow, circular, and smooth colonies on TSA medium. MK-8(H4) was the predominant menaquinone. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, and C16:0. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), an unknown phospholipid (PL1), an unknown amino lipid (AL1), and unidentified polar lipids (L1-5). The genomic DNA G+C content was 71.1 mol%. The peptidoglycan contained L-ornithine as the diagnostic diamino acid. Whole-cell sugars were composed of glucose, arabinose, and xylose. Overall, data collected from phenotypic and genotypic tests during this study indicated that strain DCY118T could not be assigned to a recognized species. Strain DCY118T showed antagonistic activity against the fungal pathogens causing root rot in ginseng, i.e., Fusarium solani (KACC 44891T) and Cylindrocarpon destructans (KACC 44660T). The results from this study confirm the DCY118T strain as a new species within the genus Ornithinimicrobium, for which the name Ornithinimicrobium panacihumi is proposed. The type strain is DCY118T (=KCTC 39962T=JCM 32156T).
Asunto(s)
Antibiosis/fisiología , Fusarium/crecimiento & desarrollo , Hypocreales/crecimiento & desarrollo , Micrococcaceae/aislamiento & purificación , Micrococcaceae/metabolismo , Panax/microbiología , Raíces de Plantas/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base/genética , ADN Bacteriano/genética , Ácidos Grasos/análisis , Micrococcaceae/clasificación , Micrococcaceae/genética , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Microbiología del SueloRESUMEN
The novel species DCY115T was isolated from ginseng-cultivated soil in Gochang province, Republic of Korea. The isolated strain was assigned to the genus Paraburkholderia due to its 16S rRNA gene sequence proximity to Paraburkholderia xenovorans LB400T (98.8%), Paraburkholderia terricola LMG 20594T (98.4%), Paraburkholderia graminis C4D1MT (98.2%), Paraburkholderia rhynchosiae WSM3937T (98.1%), and Paraburkholderia phytofirmans PsJNT (98.1%). Strain DCY115T is gram-negative, facultative aerobic, rod-shaped, non-motile, non-flagellated, and oxidase and catalase positive. The predominant isoprenoid quinone of DCY115T is ubiquinone Q-8. The major cellular fatty acids are C16:0, cyclo-C17:0, cyclo-C19:0 ω8c, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The major polar lipids include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and an unknown amino lipid (AL1). The genomic DNA G + C content is 61.3 mol%. Phenotypic tests and chemotaxonomic analysis place strain DCY115T in the genus Paraburkholderia. DNA-DNA hybridization values between strain DCY115T and closely related reference strains were lower than 51%. The low DNA relatedness data in combination with phylogenetic and biochemical tests showed that strain DCY115T could not be assigned to any recognized species. Finally, strain DCY115T showed antagonistic activity against Fusarium solani (KACC 44891T) and Cylindrocarpon destructans (KACC 44660T), which are two root rot fungal pathogens of ginseng. In conclusion, the results in this study support strain DCY115T as a novel species within the genus Paraburkholderia for which the name Paraburkholderia panacihumi is proposed. The type strain is DCY115T (= KCTC 52952T = JCM 32099T).
Asunto(s)
Antibiosis/fisiología , Burkholderiaceae/clasificación , Burkholderiaceae/aislamiento & purificación , Panax/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base/genética , Burkholderiaceae/genética , Catalasa/metabolismo , ADN Bacteriano/genética , Ácidos Grasos/análisis , Hongos/crecimiento & desarrollo , Hibridación de Ácido Nucleico , Oxidorreductasas/metabolismo , Fosfolípidos/análisis , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Microbiología del Suelo , Ubiquinona/análisisRESUMEN
A novel Gram-negative rod, endophytic bacterium, designated strain TMCC 8258T, was isolated from the root of Camellia sinensis collected from Puer, south-west China. Comparative 16S rRNA gene sequence analysis showed that the strain belongs to the family Sphingobacteriaceae and a neighbour-joining phylogenetic tree suggested that strain TMCC 8258T formed a cluster with the type strain of Olivibacter ginsengisoli (showed the highest 16S rRNA gene sequence similarity of 95.8%). Chemotaxonomic data [major fatty acid iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C17:0 3-OH and major respiratory quinone MK-7] confirmed the affiliation of strain TMCC 8258T to the genus Olivibacter. The G + C content was 39.1 mol %. The results of the phylogenetic analysis, together with the physiological, morphological and biochemical tests, suggested that strain TMCC 8258T should be classified as representing a novel species of the genus Olivibacter, for which the name Olivibacter flavus is proposed. The type strain is TMCC 8258T (=CGMCC 1.16141 = KCTC 42683).
Asunto(s)
Bacteroidetes , Camellia sinensis/microbiología , ADN Bacteriano/genética , Raíces de Plantas/microbiología , Técnicas de Tipificación Bacteriana , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Composición de Base/genética , China , Ácidos Grasos/análisis , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
A novel strain DCY105T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY105T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5-7.0 and in the absence of NaCl. Phylogenetically, strain DCY105T is most closely related to Achromobacter marplatensis LMG 26219T (96.81%). The DNA G+C content of strain DCY105T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were amongst the major polar lipids. C16:00, C8:03OH and iso-C17:03OH were identified as the major fatty acids present in DCY105T. The results of physiological and biochemical tests allowed strain DCY105T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105T (=CCTCCAB 2015193T =KCTC 42751T).
Asunto(s)
Achromobacter , Panax/microbiología , Achromobacter/clasificación , Achromobacter/genética , Achromobacter/aislamiento & purificación , Composición de Base/genética , ADN Bacteriano/genética , Ácidos Grasos/análisis , ARN Ribosómico 16S/genética , República de Corea , Rizosfera , Análisis de Secuencia de ADN , Microbiología del SueloRESUMEN
Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes. The plastome is 152,553 bp in length and includes a pair of inverted repeats (IRs) of 25,523 bp that separate a large single copy (LSC) region of 84,058 bp and a small single copy (SSC) region of 17,449 bp. It has 38.0% GC content and includes 114 unique genes, of which 80 are protein-coding, 30 are transfer RNA, and 4 are ribosomal RNA. Also, it contains 21 forward repeats, 19 palindrome repeats and 41 simple sequence repeats (SSRs). The repeats and SSRs within S. dentata were compared with those of S. takesimensis and present certain discrepancies. The chloroplast genome of S. dentata was compared with other five publicly available Lamiales genomes from different families. All the coding regions and non-coding regions (introns and intergenic spacers) within the six chloroplast genomes have been extracted and analysed. Furthermore, the genome divergent hotspot regions were identified. Our studies could provide basic data for the alpine medicinal species conservation and molecular phylogenetic researches of Scrophulariaceae and Lamiales.
Asunto(s)
Genoma del Cloroplasto/genética , Scrophularia/genética , Composición de Base/genética , Genes de Plantas/genética , Secuencias Invertidas Repetidas/genética , Repeticiones de Microsatélite/genética , Sistemas de Lectura Abierta , Filogenia , ARN de Planta/genética , ARN Ribosómico/genética , Scrophulariaceae/genética , Análisis de Secuencia de ADNRESUMEN
Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.
Asunto(s)
Perfilación de la Expresión Génica , Plantago/genética , Plantas Medicinales/genética , Análisis de Secuencia de ARN/métodos , Composición de Base/genética , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Genes de Plantas , Redes y Vías Metabólicas/genética , Repeticiones de Microsatélite/genética , Anotación de Secuencia Molecular , Motivos de Nucleótidos/genética , Proteoma/metabolismo , Control de Calidad , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN no Traducido/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Reproducción , Homología de Secuencia de Aminoácido , Programas Informáticos , Factores de Transcripción/metabolismoRESUMEN
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.
Asunto(s)
Cloroplastos/genética , ADN de Cloroplastos/genética , Morinda/genética , Composición de Base/genética , Secuencia de Bases/genética , China , Secuencia Conservada/genética , Orden Génico/genética , Genes de Plantas/genética , Genoma Mitocondrial/genética , Genoma de Planta/genética , Filogenia , Plantas Medicinales/genética , Rubiaceae/genética , Análisis de Secuencia de ADN/métodosRESUMEN
We have determined the mitochondrial genome of the first Amynthas earthworm, Amynthas aspergillus (Perrier, 1872), which is a natural medical resource in Chinese traditional medicine. Its mitogenome is 15,115 bp in length containing 37 genes with the same contents and order as other sequenced earthworms. All genes are encoded by the same strand, all 13 PCGs use ATG as start codon. The content of A + T is 63.04% for A. aspergillus (33.41% A, 29.63% T, 14.56% G and 22.41% C). The complete mitochondrial genomes of A. aspergillus would be useful for the reconstruction of Oligochaeta polygenetic relationships.
Asunto(s)
Genoma de los Insectos , Genoma Mitocondrial , Oligoquetos/genética , Animales , Composición de Base/genética , Emparejamiento Base/genética , Secuencia de Bases , ADN Mitocondrial/genética , Genes MitocondrialesRESUMEN
Slipper lobsters are a unique group of decapod crustaceans; they have cylindrical or flattened bodies and belong to the family Scyllaridae. The genus Ibacus (Leach, 1815) (Achelata, Scyllaridae, Ibacinae) consists of eight recognized species to date, all of which occur in the Indo-West Pacific Ocean and are commercially important seafood species. The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Von Siebold, 1824) is 15,696 bp in size and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 783 bp. The base composition of I. ciliatus is 35.8% A, 34.7% T, 19.0% C, and 10.5% G, with an overall AT content of 70.5%. The mitogenome of I. ciliatus was found to have gene arrangement and transcriptional polarity identical to that of the American lobster Homarus americanus, showing the pancrustacean ground pattern. Here, we present the complete mitogenome sequence of I. ciliatus; it is the first mitogenome information from the subfamily Ibacinae, and represents the second for the family Scyllaridae.
Asunto(s)
Genoma Mitocondrial , Nephropidae/genética , Animales , Composición de Base/genética , Secuencia de Bases , ADN Mitocondrial/genética , ARN Ribosómico/genética , ARN de Transferencia/genéticaRESUMEN
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.
Asunto(s)
Cloroplastos/genética , ADN de Cloroplastos/genética , Dendrobium/genética , Genoma del Cloroplasto/genética , Genoma de Planta/genética , Composición de Base/genética , Secuencia de Bases , China , Mapeo Cromosómico , Orden Génico/genética , Genes de Plantas/genética , Tamaño del Genoma/genética , Secuencias Invertidas Repetidas/genética , Medicina Tradicional China , Hojas de la Planta/genética , ARN Ribosómico/genética , ARN de Transferencia/genética , Análisis de Secuencia de ADNRESUMEN
The complete chloroplast (cp) genome sequence of Dendrobium nobile, an endangered and traditional Chinese medicine with important economic value, is presented in this article. The total genome size is 150,793 bp, containing a large single copy (LSC) region (84,939 bp) and a small single copy region (SSC) (13,310 bp) which were separated by two inverted repeat (IRs) regions (26,272 bp). The overall GC contents of the plastid genome were 38.8%. In total, 130 unique genes were annotated and they were consisted of 76 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Fourteen genes contained one or two introns.
Asunto(s)
Cloroplastos/genética , Dendrobium/genética , Genoma del Cloroplasto/genética , Composición de Base/genética , ADN de Cloroplastos/genética , Genes de Plantas/genética , Genes de ARNr/genética , Tamaño del Genoma/genética , Genoma de Planta/genética , Intrones/genética , Filogenia , ARN de Transferencia/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Análisis de Secuencia de ADN/métodos , Secuenciación Completa del Genoma/métodosRESUMEN
Spongospora subterranea is a soil-borne obligate parasite responsible for potato powdery scab disease. S. subterranea is a member of the order Plasmodiophorida, a protist taxa that is related to Cercozoa and Foraminifera but the fine details of these relationships remain unresolved. Currently there is only one available complete mtDNA sequence of a cercozoan, Bigelowiella natans. In this work, the mitochondrial sequence of a S. subterranea isolate infecting an Andean variety of S. tuberosum ssp. andigena (Diacol-Capiro) is presented. The mtDNA codes for 16 proteins of the respiratory chain, 11 ribosomal proteins, 3 ribosomal RNAs, 24 tRNAs, a RNA processing RNaseP, a RNA-directed polymerase, and two proteins of unknown function. This is the first report of a mtDNA genome sequence from a plasmodiophorid and will be useful in clarifying the phylogenetic relationship of this group to other members in the supergroup Rhizaria once more mtDNA sequences are available.