Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

doi:10.1371/journal.pone.0054808

Cited by 46 publications

(60 citation statements)

References 72 publications

(108 reference statements)

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“…They evolve more rapidly than genic sequences, and mobile genetic elements are considered as main contributors to interspecific divergence [Charlesworth et al, 1994;Piednoël et al, 2012;Novák et al, 2014]. Repetitive DNA sequences represent a good source of molecular markers including cytogenetic landmarks [Paesold et al, 2012;Čížková et al, 2013]. As previously shown, some repeats might be species-or even chromosome-specific and can be used as probes for FISH in karyotyping, providing new insights into the evolutionary origins of species [Hobza et al, 2006;Paux et al, 2006;Dodsworth et al, 2015].…”

Section: Discussionmentioning

confidence: 99%

Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

Křivánková

Kopecký²,

Stočes³

et al. 2017

Cytogenet Genome Res

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FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F. pratensis were used as probes for FISH to develop the molecular karyotype of meadow fescue and to reveal a long-range molecular organization of its chromosomes. Five tandem repeats produced specific patterns on individual chromosomes. Their use in combination with probes for rRNA genes enabled the establishment of the molecular karyotype of meadow fescue. Most of the mobile genetic elements were dispersed along all the chromosomes except for the DNA transposon CACTA, which was localized preferentially to telomeric and subtelomeric regions, and a putative LTR element, which was localized to (peri)centromeric regions. Cytogenetic mapping of the 5 tandem repeats in other accessions of meadow fescue showed a highly similar distribution and confirmed the versatility and robustness of these probes.

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Section: Discussionmentioning

confidence: 99%

Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

Křivánková

Kopecký²,

Stočes³

et al. 2017

Cytogenet Genome Res

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“…The intention here is not to make an extensive and rigorous review of the amount of each satellite DNA studied, partly because the data are not always available, but it can be stated that the genomic content of a satellite DNA can range from 0.1% of the FriSAT1 satellite DNA in several Fritillaria species or 0.3% of satellite DNAs within the genome in Musa [Hribová et al, 2010;Čížková et al, 2013] to 36% of FriSAT1 in F. falcate [Ambrožová et al, 2011]. The relative proportions that a satellite DNA represents in the different genomes are data that must be treated with caution, but it is clear that the amount of satellite DNA present in a genome may be partly responsible for the genome size.…”

Section: Satellite Dna a Family Of Sequences That Get On Well With Ementioning

confidence: 99%

“…In rice and maize, for example, all centromeres have different retrotransposon families [Nagaki et al, 2005;Bao et al, 2006]. Furthermore, retrotransposons are the main component of banana and some wheat centromeres [Čížková et al, 2013;Li et al, 2013].…”

Section: Plant Centromere and The Pericentromeric Regionmentioning

confidence: 99%

Satellite DNA in Plants: More than Just Rubbish

Garrido-Ramos

2015

Cytogenet Genome Res

150

149

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For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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“…While the implication in previous studies (Heslop-Harrison & Schwarzacher, 2007;Howell, Newbury, Swennen, Whithers, & Ford-Lloyd, 1994;Nwakanma, Pillay, Okoli, & Tenkouano, 2003;Nair, Teo, & Schwarzacher, Heslop-Harisson, 2005) alluded marked differentiation of the A and B genomes, the SC3 primers developed in this study from the A genome do not suggest such a differentiation. Evidence for the lack of complete differentiation of the A and B genomes of banana does exist in the literature (Ortiz & Vuylsteke, 1994;Osuji, Harrison, Crouch, & Heslop-Harrison, 1997;D'Hont, Paget-Goy, Escoute, & Carreel, 2000;Khayat, 2004;Boonruangrod, Desai, Fluch, Berenyi, & Burg, 2008;Jeridi et al, 2011Jeridi et al, , 2012Cizkova et al, 2013;De Jesus et al, 2013). The first study that alluded to the lack of differentiation between the A and B genomes was that of (Nair, Teo, Schwarzacher, & Heslop-Harisson, 2005).…”

Section: Discussmentioning

confidence: 99%

“…In a subsequent study, Jeridi et al (2011) used cytogenetic evidence of mixed disomic and polysomic inheritance to suggest that there are chromosome exchanges between M. acuminata (AA) and M. balbisiana (BB). Cizkova et al (2013) used flow cytometry, ITS and SSR to support their hypothesis that recombination does occur between the A and B genomes of banana. Finally, the study by Jeridi et al (2012) on the organization of DNA satellites in banana showed that two satellites derived from M. acuminata were widespread in M. balbisiana and a number of ABB hybrids and the S genome.…”

Section: Discussmentioning

confidence: 99%

SCAR Marker for the A Genome of Bananas (Musa spp. L.) Supports Lack of Differentiation between the A and B Genomes

Mabonga¹,

Pillay²

2017

JAS

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Bananas (Musa spp. L.) are grouped on the basis of their genomic origins in relation to Musa acuminata (A genome) and M. balbisiana (B genome). The two ancestral wild seeded diploid species evolved in vastly different geographical areas and contributed several agronomic traits towards the present genetic composition of cultivated bananas. Most cultivated bananas are triploid (AAA, AAB and ABB), some are diploid (AA, BB and AB) and a few are tetraploids (AAAA, AAAB, AABB and ABBB). Limitations on the correct identification of the A and B genomes in Musa have generated need for the development of new and more reliable techniques. Distinguishing the A and the B genome remains practically and theoretically important for banana breeders. The aim of the research was to develop a DNA based A genome specific marker for the identification of the A genome in bananas. A putative marker (600 bp) specific to the A genome was identified by Random Amplified Polymorphic DNA (RAPD) technique. A sequence characterised amplified region (SCAR) marker was developed from the RAPD amplicon. The SCAR primers annealed a 500 bp fragment specific to the A genome in a sample of 22 randomly selected homo-and heterogenomic A genome containing accessions representing different genome combinations. The 500 bp SCAR marker is useful for the identification of the A genome. However an additional 700 bp fragment annealed in all M. balbisiana genotypes and in five of the eight heterogenomic accessions, suggesting lack of differentiation between the A and B genome. This study has provided a 500 bp A genome SCAR marker and recent evidence that the A and B genomes of banana may not be as differentiated as previously considered.

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Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

Cited by 46 publications

References 72 publications

Repetitive DNA: A Versatile Tool for Karyotyping in<b><i> Festuca pratensis</i></b> Huds.

Repetitive DNA: A Versatile Tool for Karyotyping in<b><i> Festuca pratensis</i></b> Huds.

Satellite DNA in Plants: More than Just Rubbish

SCAR Marker for the A Genome of Bananas (Musa spp. L.) Supports Lack of Differentiation between the A and B Genomes

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