Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

16S ribosomal DNA characterization of nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril).

ABSTRACT: Nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis. Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans, Burkholderia brasilensis, and Burkholderia tropicalis were identified. Eight other types were placed in close proximity to these genera and other alpha and beta Proteobacteria.

SUBMITTER: Magalhaes Cruz L

PROVIDER: S-EPMC92882 | biostudies-literature | 2001 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

16S ribosomal DNA characterization of nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril).

Magalhães Cruz L L de Souza E M EM Weber O B OB Baldani J I JI Döbereiner J J Pedrosa F de O Fde O

Applied and environmental microbiology 20010501 5

Nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis. Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans, Burkholderia brasilensis, and Burkholderia tropicalis were identified. Eight other types were placed in close proximity to these genera and other alpha and beta Proteobacteria. ...[more]

PMID: 11319127

Similar Datasets

Draft Genome Sequences of Dickeya Species Associated with Soft Rot Diseases in Pineapple (Ananas comosus) and Banana (Musa spp.).

Project description:Dickeya species cause soft rots on many commercial crops. Here, we present the draft genomes of Dickeya oryzae (BRIP 64262) and Dickeya zeae (BRIP 64263) isolates causing soft rot on banana (Musa spp.) and pineapple (Ananas comosus) plants, respectively. This expands the range of available genomes from plant-pathogenic Dickeya species.

| S-EPMC9670999 | biostudies-literature

Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm.

Project description:Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. 'Cayenne', 'Spanish', 'Queen') was not well supported by the present study. These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

| S-EPMC4660223 | biostudies-literature

Genome sequence of pineapple secovirus B, a second sadwavirus reported infecting Ananas comosus.

Project description:The complete genome sequence of pineapple secovirus B (PSV-B), a new virus infecting pineapple (Ananas comosus) on the island of Oahu, Hawaii, was determined by high-throughput sequencing (HTS). The genome comprises two RNAs that are 5,956 and 3,808 nt long, excluding the 3'-end poly-A tails, both coding for a single large polyprotein. The RNA1 polyprotein contains five conserved domains associated with replication, while the RNA2 polyprotein is cleaved into the movement protein and coat protein. PSV-B is representative of a new species in the subgenus Cholivirus (genus Sadwavirus; family Secoviridae), as the level of amino acid sequence identity to recognized members of this subgenus in the Pro-Pol and coat protein regions is below currently valid species demarcation thresholds.

| S-EPMC9741570 | biostudies-literature

Nanoapplication of a Resistance Inducer to Reduce Phytophthora Disease in Pineapple (Ananas comosus L.).

Project description:Treatment of plants with a variety of abiotic and biotic inducers causes induced resistance to pathogen attack. In this study, the effect of four resistance inducers on plant diseases caused by Phytophthora cinnamomi was screened in vivo initially by using lupin, a susceptible model plant. Lupin pretreated with 0.5 mM salicylic acid (SA) showed effective resistance against P. cinnamomi with restricted lesions. Then, mesoporous silica nanoparticles (MSNs) with particle size around 20 nm and approximate pore size of 3.0 nm were synthesized and functionalized for loading and importing SA to pineapple plantlets. Decanethiol gatekeepers were introduced to the surface of MSNs via glutathione (GSH)-cleavable disulfide linkages to cover the pore entrance, which was confirmed through using Raman spectroscopy. Through free diffusion, the loading efficiency of SA in MSNs gated with gatekeepers was 11.7%, but was lower in MSNs without gatekeepers (8.0%). In addition, in vitro release profile of SA from gatekeeper-capped MSNs indicated that higher concentrations of GSH resulted in more cargo release. Moreover, the experiments in planta showed that the application of MSNs as a resistance inducer delivery system significantly improved pineapple resistance to P. cinnamomi in terms of inhibiting lesion development and improving root growth of infected plants, compared to the use of free SA and MSNs without gatekeepers. The analysis of SA, GSH, and defense-related genes, of PR1 and PR5, further confirmed that the slow and prolonged release of SA from MSNs inside the roots of pineapple plants was achieved through a redox-stimuli release mechanism. Therefore, the application of MSNs with redox-responsive gatekeepers has shown great potential as an efficient tool for delivering chemicals into plants in a controllable way.

| S-EPMC6797602 | biostudies-literature

GC-MS Based Metabolite Profiling to Monitor Ripening-Specific Metabolites in Pineapple (Ananas comosus).

Project description:Pineapple is one of the most cultivated tropical, non-climacteric fruits in the world due to its high market value and production volume. Since non-climacteric fruits do not ripen after harvest, the ripening stage at the time of harvest is an important factor that determines sensory quality and shelf life. The objective of this research was to investigate metabolite changes in the pineapple ripening process by metabolite profiling approach. Pineapple (Queen variety) samples from Indonesia were subjected to GC-MS analysis. A total of 56, 47, and 54 metabolites were annotated from the crown, flesh, and peel parts, respectively. From the principal component analysis (PCA) plot, separation of samples based on ripening stages from C0-C2 (early ripening stages) and C3-C4 (late ripening stages) was observed for flesh and peel parts, whereas no clear separation was seen for the crown part. Furthermore, orthogonal projection to latent structures (OPLS) analysis suggested metabolites that were associated with the ripening stages in flesh and peel parts of pineapple. This study indicated potentially important metabolites that are correlated to the ripening of pineapple that would provide a basis for further study on pineapple ripening process.

| S-EPMC7240947 | biostudies-literature

Multidisciplinary perspectives on banana (Musa spp.) domestication.

Project description:Original multidisciplinary research hereby clarifies the complex geodomestication pathways that generated the vast range of banana cultivars (cvs). Genetic analyses identify the wild ancestors of modern-day cvs and elucidate several key stages of domestication for different cv groups. Archaeology and linguistics shed light on the historical roles of people in the movement and cultivation of bananas from New Guinea to West Africa during the Holocene. The historical reconstruction of domestication processes is essential for breeding programs seeking to diversify and improve banana cvs for the future.

| S-EPMC3136277 | biostudies-literature

Cloning and expression analysis of a PISTILLATA homologous gene from pineapple (Ananas comosus L. Merr).

Project description:PISTILLATA (PI)-like genes are crucial regulators of flowering in angiosperms. A homologue of PI, designated as AcPI (Genbank accession number HQ717796), was isolated from pineapple cultivar Comte de Paris by reverse transcriptase polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The cDNA sequence of AcPI is 907 bp in length and contains an open reading frame of 594 bp, which encodes a protein of 197 amino acids. The molecular weight was 2.29 kDa and the isoelectric point was 9.28. The alignment showed that AcPI had a high identity with CsPIC2 (78.6%), AoPI (77.4%), OrcPI (75.7%) and HPI2 (72.4%). Quantitative real-time polymerase chain reaction (qRT-PCR) analyses in different tissues showed that the expression pattern of AcPI was different from the B-class genes in eudicots. AcPI was expressed in all the tissues investigated. The expression level was very low in fruit stems, bracts, leaves and sepals, high in petals and carpels, and moderate in apical meristems, flesh and stamens. The qRT-PCR analyses in different stages indicated that the expression of AcPI reached the highest level at 40 days after flower inducement, when the multiple fruit and floral organs were forming. It proved the important role of AcPI in floral organs and fruit development. The 35S::AcPI transgenic Arabidopsis plants flowered earlier and had more inflorescences or branches than wild type plants.

| S-EPMC3269737 | biostudies-literature

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

Project description:To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

| S-EPMC4482178 | biostudies-literature

Yield gap reduction of pineapple (Ananas comosus L.) by site-specific nutrient management.

Project description:Acid-sulfate soils and overuse of chemical fertilizers have been obstacles to sustainable agriculture. The variation of fertilization due to poor soil fertility has remarkably affected the yield gap and the quality of the environment, so an optimal fertilizing rate should be formulated. Therefore, this study aimed at (i) detecting obstacles in soil characteristics reducing pineapple yield between farms and (ii) assessing the effects of NPKCaMg fertilizers on soil fertility, uptakes, and pineapple yield. The on-farm experiment was carried out according to site-specific nutrient management (SSNM) arranging in acid-sulfate soil for pineapple, including (i) no fertilizers used; (ii) NPKCaMg: fully fertilizing with nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg); (ii) PKCaMg: fertilizing without N; (iii) NKCaMg: fertilizing without P; (iv) NPCaMg: fertilizing without K; (v) NPKMg: fertilizing without Ca; (vi) NPKCa: fertilizing without Mg; and (vii) FFP: farmers' fertilizing practice. The result of the principal component analysis revealed that the soil had low availability of N, P, and K nutrients. Available P concentration was negatively correlated with concentrations of Al3+, Fe2+, and total Mn, whose correlation coefficients were -0.34 to -0.59, -0.52 to -0.74, and -0.63 to -0.70, respectively. Fertilizing NPKCaMg obtained the highest result in the uptakes of N, P, K, Ca, and Mg, which were 289.1-327.4, 25.4-29.3, 137.4-166.0, 41.9-48.9, and 39.8-43.1 kg ha-1, respectively. Fertilizing by SSNM has increased pineapple yield by 22.9 %-44.9 % compared to the FFP. This fertilizer formula should be transferred to the local farmers in order not only to enhance productivity, but also to limit the damage of chemical fertilizers on the environment. Moreover, this formula should be tested globally in other places that share similar soil characteristics.

| S-EPMC10864984 | biostudies-literature

SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr.

Project description:Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ platform. Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions 'MD-2' and 'Yonekura'. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future.

| S-EPMC7372017 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data