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At least 19 recordsLinked to original sources

PubMed1997

Characterization of a linear DNA plasmid from the filamentous fungal plant pathogen Glomerella musae [Anamorph: Colltotrichum musae (Berk. & Curt.) Arx.].

A 7.4-kilobase (kb) DNA plasmid was isolated from Glomerella musae isolate 927 and designated pGML1. Exonuclease treatments indicated that pGML1 was a linear plasmid with blocked 5' termini. Cell-fractionation experiments combined with sequence-specific PCR amplification revealed that pGML1 resided in mitochondria. The pGML1 plasmid hybridized to cesium chloride-fractionated nuclear DNA but not to A + T-rich mitochondrial DNA. An internal 7.0-kb section of pGML1 was cloned and did not hybridize with either nuclear or mitochondrial DNA from G. musae. Sequence analysis revealed identical terminal inverted repeats (TIR) of 520 bp at the ends of the cloned 7.0-kb section of pGML1. The occurrence of pGML1 did not correspond with the pathogenicity of G. musae on banana fruit. Four additional isolates of G. musae possessed extrachromosomal DNA fragments similar in size and sequence to pGML1.

Ascomycota↗

PubMed2002

Genetic Diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP Markers.

Genetic diversity and relationships were assessed in 28 accessions of Musa acuminata (AA) Colla and Musa balbisiana (BB) Colla, and some of their natural hybrids, using the amplified fragment length polymorphisms (AFLP) technique. Fifteen AFLP +3 primer pairs produced 527 polymorphic bands among the accessions. Neighbor-joining and principal co-ordinate (PCO) analyses using Jaccard's similarity coefficient produced four major clusters that closely corresponded with the genome composition of the accessions (AA, BB, AAB and ABB). The AFLP data distinguished between the wild diploid accessions and suggested new subspecies relationships in the M. acuminata complex that are different from those based on morphological data. The data suggested that there are three subspecies within the M. acuminata complex (ssp. burmannica Simmonds, malaccensis Simmonds, and microcarpa Simmonds). 'Tjau Lagada' (ssp. microcarpa), 'Truncata' [ssp truncata (Ridl.) Shepherd] and 'SF247' [ssp. banksii (F.Muell) Simmonds] clustered very closely with 'Gros Michel' and 'Km 5', indicating that more than one M. acuminata subspecies may be involved in the origin of triploid AAA bananas. 'Calcutta 4' (ssp. burmannicoides De Langhe & Devreux) and 'Long Tavoy' (ssp. burmannica) were closely related and could be together in the same subspecies. This study also showed that there is much more genetic diversity within M. balbisiana that was split into two groups: (1) 'I-63' and 'HND' and (2) 'Los Banos', 'MPL' (Montpellier), '10852', 'Singapuri', 'Etikehel', and 'Butohan 1' as the other.

Journal Article↗

PubMed2003

Sectional relationships in the genus Musa L. inferred from the PCR-RFLP of organelle DNA sequences.

The objective of this study was to construct a molecular phylogeny of the genus Musa using restriction-site polymorphisms of the chloroplast (cpDNA) and mitochondrial DNA (mtDNA). Six cpDNA and two mtDNA sequences were amplified individually in polymerase chain reaction (PCR) experiments in 13 species representing the four sections of Musa. Ensete ventricosum (W.) Ch. was used as the outgroup. The amplified products were digested with ten restriction endonucleases. A total of 79 restriction-site changes were scored in the sample. Wagner parsimony using the branch and bound option defined two lines of evolution in Musa. One lineage comprised species of the sections Australimusa and Callimusa which have a basic number of x = 10 chromosomes, while most species of sections Eumusa and Rhodochlamys ( x = 11) formed the other lineage. Musa laterita Cheesman ( Rhodochlamys) had identical organellar genome patterns as some subspecies of the Musa acuminata Colla complex. The progenitors of the cultivated bananas, M. acuminata and Musa balbisiana Colla, were evolutionarily distinct from each other. Musa balbisiana occupied a basal position in the cladogram indicating an evolutionarily primitive status. The close phylogenetic relationship between M. laterita and M. acuminata suggests that species of the section Rhodochlamys may constitute a secondary genepool for the improvement of cultivated bananas.

DNA Probes↗

PubMed2001

Nuclear DNA content and base composition in 28 taxa of Musa.

The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

Algorithms↗

PubMed2002

Identification of genetic markers linked to banana streak disease expression in inter-specific Musa hybrids.

Recently-introduced inter-specific Musa hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with banana streak virus (BSV), the causal agent of banana streak disease (BSD). One hypothesis suggests: (1) that BSD occurrence in these inter-specific hybrids results from activation of BSV-Ol endogenous pararetrovirus sequences (EPRV) integrated into the Musa genome rather than from external sources of infection, and (2) that the process of genetic hybridisation may be one factor involved in triggering episomal expression of the BSV integrants. In order to test this hypothesis we carried out a genetic analysis of BSD incidence in a F1 triploid ( Musa AAB) population produced by inter-specific hybridisation between virus and disease-free diploid Musa balbisiana (BB) and tetraploid Musa acuminata (AAAA) parents. Half of the F1 progeny of this cross expressed BSV particles. Using PCR amplification to determine the presence or absence of BSV-Ol EPRVs, it was determined that this endogenous sequence was specific to the M. babisiana genome and occurred in a homozygous state. Using bulk segregant analysis, ten AFLP markers co-segregating with the absence and/or presence of BSV infection were identified in the M. balbisiana genome, but were absent from the M. acuminata genome. Seven of these markers segregated with the presence of a BSV particle and three with the absence of BSV particles. Analysis of the segregation of these markers using a test-cross configuration allowed the construction of a genetic map of the linkage group containing the locus associated with BSV infection in the F1 hybrid population. These data indicate that a genetic mechanism is involved in BSV appearance, and suggest that a monogenic allelic system confers the role of carrier to the M. balbisiana parent.

Alleles↗

PubMed2002

Analysis of genetic diversity and sectional relationships in Musa using AFLP markers.

The AFLP technique was used to assess the genetic diversity and sectional relationships in 39 accessions representing the four main sections of the genus Musa. Eight AFLP + 3 primer pairs produced 260 polymorphic bands that were used in cluster and PCO analysis. A wide range of variability was observed among the species within the sections of the genus Musa. AFLP data was useful in separating the different sections of the genus as well as differentiating the different genomic groups of section Eumusa. Section Rhodochlamys ( x = 11) appeared as a distinct entity and clustered closely with the Musa acuminata Colla complex of section Eumusa that has the same basic chromosome number. This relationship is congruent with previous studies. However, unlike previous proposals that questioned the identity of Rhodochlamys as a separate taxonomic unit, PCO analysis of the AFLP data showed that it is a distinct entity. Musa laterita Cheesman ( Rhodochlamys) and Musa schizocarpa Simmonds clustered with the M. acuminata complex suggesting that they may be sources of useful genes for the improvement of the cultivated bananas. Callimusa formed a distinct unit and was closer to Australimusa than to the other sections. Although both sections share the same basic chromosome number of x = 10 these sections are genetically distinct

Journal Article↗

PubMed2003

PCR-RFLP of the ribosomal DNA internal transcribed spacers (ITS) provides markers for the A and B genomes in Musa L.

Musa acuminata Colla (AA genomes) and Musa balbisiana Colla (BB genomes) are the diploid ancestors of modern bananas that are mostly diploid or triploid cultivars with various combinations of the A and B genomes, including AA, AAA, BB, AAB and ABB. The objective of this study was to identify molecular markers that will facilitate discrimination of the A and B genomes, based on restriction-site variations in the internal transcribed spacers (ITS) of the nuclear ribosomal RNA genes. The ITS regions of seven M. acuminata and five M. balbisiana accessions were each amplified by PCR using specific primers. All accessions produced a 700-bp fragment that is equivalent in size to the ITS of most plants. This fragment was then digested with ten restriction enzymes ( AluI, CfoI, DdeI, HaeIII, HinfI, HpaII, MspI, RsaI, Sau3AI and TaqI) and fractionated in 2% agarose gels, stained with ethidium bromide and visualized under UV light. The RsaI digest revealed a single 530-bp fragment unique to the A genome and two fragments of 350-bp and 180-bp that were specific to the B genome. A further 56 accessions representing AA, AAA, AAB, AB and ABB cultivars, and synthetic hybrids, were amplified and screened with RsaI. All accessions with an exclusively A genome showed only the 530-bp fragment, while accessions having only the B-genome lacked the 530-bp fragment but had the 350-bp and 180-bp fragments. Interspecific cultivars possessed all three fragments. The staining intensity of the B-genome markers increased with the number of B-genome complements. These markers can be used to determine the genome constitution of Musa accessions and hybrids at the nursery stage, and, therefore, greatly facilitate genome classification in Musa breeding.

Chimera↗

PubMed2002

Ascertaining maternal and paternal lineage within Musa by chloroplast and mitochondrial DNA RFLP analyses.

In banana, the maternal transmission of chloroplast DNA and paternal transmission of the mitochondrial DNA provides an exceptional opportunity for studying the maternal and paternal lineage of clones. In the present study, RFLP combined with hybridization of heterologous mitochondrial and chloroplastic probes have been used to characterize 71 wild accessions and 131 diploid and 103 triploid cultivated clones. In additon to Musa acuminata and Musa balbisiana, other species from the four Musa sections were studied to investigate their contribution to the origin of cultivated bananas. These molecular analyses enable the classification of the Musa complex to be discussed. Results ascertain relationships among and between the wild accessions and the mono- and interspecific diploid and triploid bananas, particularly for the acuminata genome. Parthenocarpic varieties are shown to be linked to M. acuminata banksii and M. acuminata errans, thus suggesting that the first center of domestication was in the Philippines - New Guinea area.

DNA Probes↗

PubMed2005

Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications.

Nuclear DNA content and genomic distributions of 5S and 45S rDNA were examined in nineteen diploid accessions of the genus Musa representing its four sections Eumusa, Rhodochlamys, Callimusa and Australimusa, and in Ensete gilletii, which was the outgroup in this study. In the Eumusa (x = 11), 2C DNA content ranged from 1.130 to 1.377 pg, M. balbisiana having the lowest DNA content of all sections. M. beccarii (x = 9), a representative of Callimusa, had the highest 2C nuclear DNA content (1.561 pg). Species belonging to Rhodochlamys (x = 11) and Australimusa (x = 10) had 2C DNA contents ranging from 1.191 to 1.299 pg and from 1.435 to 1.547 pg, respectively. E. gilletii (x = 9) had 2C DNA content of 1.210 pg. The number of 5S rDNA loci in Musa varied from 4 to 8 per diploid cell. While different numbers of 5S rDNA loci were observed within Eumusa and Rhodochlamys, four 5S rDNA loci were observed in all accessions of Australimusa. M. beccarii (Callimusa) and E. gilletii contained 5S rRNA gene clusters on five and six chromosomes, respectively. The number of 45S rDNA loci was conserved within individual sections. Hierarchical cluster analysis of genome size, number of chromosomes and 45S rDNA sites suggested a close relationship between Rhodochlamys and Eumusa; Australimusa was clearly separated as were M. beccarii and E. gilletii. Within the Eumusa-Rhodochlamys group, M. balbisiana, M. schizocarpa and M. ornata formed distinct subgroups, clearly separated from the accessions of M. acuminata, M. mannii, M. laterita and M. velutina, which formed a tight subgroup. The results expand the knowledge of genome size and genomic distribution of ribosomal DNA in Musa and Ensete. They aid in clarification of the taxonomical classification of Musa and show a need to supplement the analyses on the DNA sequence level with cytogenetic studies.

Cell Nucleus↗

PubMed2002

Rapid detection of aneuploidy in Musa using flow cytometry.

We report a procedure for the rapid and convenient detection of aneuploidy in triploid Musa using DNA flow cytometry. From a population of plants derived from gamma-irradiated shoot tips, plants were selected based on aberrant morphology and their chromosome numbers were counted. Aneuploids plants with chromosome numbers 2n=31 or 32 were found as well as the expected triploid plants (2n=3x=33). At the same time, the nuclear DNA content of all plants was measured using flow cytometry. The flow cytometric assay involved the use of nuclei isolated from chicken red blood cells (CRBC), which served as an internal reference standard. The relative DNA content of individual plants was expressed as a ratio of DNA content of CRBC and Musa (DNA index). In order to estimate the chromosome number using flow cytometry, the relative DNA content of plants with unknown ploidy was expressed as a percentage of the DNA content of triploid plants. The classification based on flow cytometry fully agreed with the results obtained by chromosome counting. The results indicated that flow cytometry is a convenient and rapid method for the detection of aneuploidy in Musa.

Aneuploidy↗

PubMed2005

Neutralizing properties of Musa paradisiaca L. (Musaceae) juice on phospholipase A2, myotoxic, hemorrhagic and lethal activities of crotalidae venoms.

The use of plants as medicine has been referred to since ancient peoples, perhaps as early as Neanderthal man. Plants are a source of many biologically active products and nowadays they are of great interest to the pharmaceutical industry. The study of how people of different culture use plants in particular ways has led to the discovery of important new medicines. In this work, we verify the possible activity of Musa paradisiaca L. (Musaceae) against the toxicity of snake venoms. Musa paradisiaca, an important source of food in the world, has also been reported to be popularly used as an anti-venom. Interaction of Musa paradisiaca extract (MsE) with snake venom proteins has been examined in this study. Phospholipase A2 (PLA2), myotoxic and hemorrhagic activities, including lethality in mice, induced by crotalidae venoms were significantly inhibited when different amounts of MsE were mixed with these venoms before assays. On the other hand, mice that received MsE and venoms without previous mixture or by separated routes were not protected against venom toxicity. Partial chemical characterization of MsE showed the presence of polyphenols and tannins and they are known to non-specifically inactivate proteins. We suggest that these compounds can be responsible for the in vitro inhibition of the toxic effects of snake venoms. In conclusion, according to our results, using mice as experimental model, MsE does not show protection against the toxic effects of snake venoms in vivo, but if was very effective when the experiments were done in vitro.

Animals↗

PubMed2002

Isolation, characterization and chromosome localization of repetitive DNA sequences in bananas (Musa spp.).

Partial genomic DNA libraries were constructed in Musa acuminata and M. balbisiana and screened for clones carrying repeated sequences, and sequences carrying rDNA. Isolated clones were characterized in terms of copy number, genomic distribution in M. acuminata and M. balbisiana, and sequence similarity to known DNA sequences. Ribosomal RNA genes have been the most abundant sequences recovered. FISH with probes for DNA clones Radkal and Radka7, which carry different fragments of Musa 26S rDNA, and Radka14, for which no homology with known DNA sequences has been found, resulted in clear signals at secondary constrictions. Only one clone carrying 5S rDNA, named Radka2, has been recovered. All remaining DNA clones exhibited more or less pronounced clustering at centromeric regions. The study revealed small differences in genomic distribution of repetitive DNA sequences between M. acuminata and M. balbisiana, the only exception being the 5S rDNA where the two Musa clones under study differed in the number of sites. All repetitive sequences were more abundant in M. acuminata whose genome is about 12% larger than that of M. balbisiana. While, for some sequences, the differences in copy number between the species were relatively small, for some of them, e.g. Radka5, the difference was almost thirty-fold. These observations suggest that repetitive DNA sequences contribute to the difference in genome size between both species, albeit to different extents. Isolation and characterization of new repetitive DNA sequences improves the knowledge of long-range organization of chromosomes in

Chromosome Mapping↗

PubMed2002

Assessment of the validity of the sections in Musa (musaceae) using AFLP.

Musa L. (Musaceae) is currently separated into five sections (Musa. Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on chromosome numbers and morphological characters. However, the validation of this classification system is questioned due to the common occurrence of hybridizations across sections and the system not accommodating anomalous species. This study employed amplified fragment length polymorphism (AFLP) in a phenetic examination of the relationships among four sections (material of sect. Ingentimusa was not available) to evaluate whether their genetic differences justify distinction into separate groups. Using eight primer combinations, a total of 276 bands was scored, of which 275 were polymorphic. Among the monomorphic bands, 11 unique markers were identified that revealed the distinct separation of the 11-chromosome species from the 10-chromosome species. AFLP results suggest that species of sect. Rhodochlamys should be combined into a single section with species of sect. Musa, and likewise for species of sect. Australimnusa to be merged with those of sect. Callimusa.

Chromosomes↗

PubMed2004

Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome.

The first bacterial artificial chromosome (BAC) library of the banana species Musa balbisiana 'Pisang Klutuk Wulung' (PKW BAC library) was constructed and characterized. One improved and one novel protocol for nuclei isolation were employed to overcome problems caused by high levels of polyphenols and polysaccharides present in leaf tissues. The use of flow cytometry to purify cell nuclei eliminated contamination with secondary metabolites and plastid DNA. Furthermore, the usefulness of the inducible pCC1BAC vector to obtain a higher amount of BAC DNA was demonstrated. The PKW BAC library represents nine haploid genome equivalents of M. balbisiana and its mean insert size is 135 kb. It consists of two sublibraries, of which the first one (SN sublibrary with 24,960 clones) was prepared according to an improved standard nuclei isolation protocol, whereas the second (FN sublibrary with 11,904 clones) was obtained from flow-sorted nuclei. Screening with 12 RFLP probes, which were genetically anchored to 8 genetic linkage groups of the banana species Musa acuminata, revealed an average of 11 BAC clones per probe, thus confirming the genome coverage estimated based on the insert size, as well as a high level of conservation between the two species of Musa. Localization of selected BAC clones to mitotic chromosomes using FISH indicated that the BAC library represented a useful resource for cytogenetic mapping. As the first step in map-based cloning of a genetic factor that is involved in the activation of integrated pararetroviral sequences of Banana streak virus (BSV), the BSV expressed locus (BEL) was physically delimited. The PKW BAC library represents a publicly available tool, and is currently used to reveal the integration and activation mechanisms of BSV sequences and to study banana genome structure and evolution.

Cell Nucleus↗

PubMed1999

Integration of banana streak badnavirus into the Musa genome: molecular and cytogenetic evidence.

Breeding and tissue culture of certain cultivars of bananas (Musa) have led to high levels of banana streak badnavirus (BSV) infection in progeny from symptomless parents. BSV DNA hybridized to genomic DNA of one such parent, Obino l'Ewai, suggesting integration of viral sequences. Sequencing of clones of Obino l'Ewai genomic DNA revealed an interface between BSV and Musa sequences and a complex BSV integrant. In situ hybridization revealed two different BSV sequence locations in Obino l'Ewai chromosomes and a complex arrangement of BSV and Musa sequences was shown by probing stretched DNA fibers. This is the first report of integrated sequences that possibly lead to a plant pararetrovirus episomal infection by a mechanism differing markedly from animal retroviral systems.

Badnavirus↗

PubMed1999

Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences.

When some virus- and disease-free Musa spp. (banana and plantain) are propagated by tissue culture, the resulting plants develop infections with banana streak badnavirus (BSV), a pararetrovirus. In sharp contrast to the virion DNA recovered from natural infections, the virion DNA from tissue culture-associated infections of different Musa spp. was highly similar if not identical. Although BSV does not employ integration during the infection cycle, BSV DNA was found to be integrated into the Musa genome. While one integration consisted of a partial BSV genome, a second contained more than one complete genome that was almost identical to BSV recovered from tissue culture-derived plants. The arrangement of this integrated BSV DNA suggests that it can yield an infectious episomal genome via homologous recombination. This report documents the first instance of integrated DNA of a nonintegrating virus giving rise to an episomal viral infection and identifies tissue culture as a possible trigger for the infection, raising the question of whether similar activatable viral sequences exist in the genomes of other plants and animals.

Badnavirus↗

PubMed1992

Oligonucleotide and amplification fingerprinting of wild species and cultivars of banana (Musa spp.).

DNA oligonucleotide and amplification fingerprinting have been successfully used to detect genetic polymorphisms in 15 representative species and cultivars of the genus Musa, comprising AA, AAA, AAAA, AAB, ABB, and BB genotypes. In-gel-hybridization of Hinf I-digested genomic banana DNA to the 32P-labeled synthetic oligonucleotides (GATA)4, (GTG)5, and (CA)8 revealed considerable polymorphisms between Musa species and cultivars. The fingerprint patterns proved to be somatically stable and did not show differences between individual plants of 'Grand Nain' (AAA genotype). Dendrograms based on oligonucleotide fingerprint band sharing data proved to be consistent with most of the known features of the history of banana and plantain cultivation and evolution, respectively. DNA samples from the same banana species and cultivars were also amplified by PCR using single or pairwise combinations of short oligonucleotide primers. Amplification products were separated on agarose or polyacrylamide gels and visualized by ethidium bromide or silver staining, respectively. Polymorphic patterns were obtained with some but not all primers. By using the CCCTCTGCGG primer in simplex and/or duplex PCR, the induced mutant 'GN60A' was clearly recognized from its original variety 'Grand Nain'. Both fingerprint techniques allowed the detection of bands characteristic for the A and B genome. This DNA fingerprinting technology has potential application in several areas of Musa improvement.

Base Sequence↗

PubMed2006

MUSA: a parameter free algorithm for the identification of biologically significant motifs.

MOTIVATION: The ability to identify complex motifs, i.e. non-contiguous nucleotide sequences, is a key feature of modern motif finders. Addressing this problem is extremely important, not only because these motifs can accurately model biological phenomena but because its extraction is highly dependent upon the appropriate selection of numerous search parameters. Currently available combinatorial algorithms have proved to be highly efficient in exhaustively enumerating motifs (including complex motifs), which fulfill certain extraction criteria. However, one major problem with these methods is the large number of parameters that need to be specified. RESULTS: We propose a new algorithm, MUSA (Motif finding using an UnSupervised Approach), that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders. This method relies on a biclustering algorithm that operates on a matrix of co-occurrences of small motifs. The performance of this method is independent of the composite structure of the motifs being sought, making few assumptions about their characteristics. The MUSA algorithm was applied to two datasets involving the bacterium Pseudomonas putida KT2440. The first one was composed of 70 sigma(54)-dependent promoter sequences and the second dataset included 54 promoter sequences of up-regulated genes in response to phenol, as suggested by quantitative proteomics. The results obtained indicate that this approach is very effective at identifying complex motifs of biological significance. AVAILABILITY: The MUSA algorithm is available upon request from the authors, and will be made available via a Web based interface.

Algorithms↗