Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)
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{"title"=>"Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)", "type"=>"journal", "authors"=>[{"first_name"=>"Jana", "last_name"=>"Čížková", "scopus_author_id"=>"44861095300"}, {"first_name"=>"Eva", "last_name"=>"Hřibová", "scopus_author_id"=>"24467719600"}, {"first_name"=>"Lenka", "last_name"=>"Humplíková", "scopus_author_id"=>"57199676756"}, {"first_name"=>"Pavla", "last_name"=>"Christelová", "scopus_author_id"=>"36491243500"}, {"first_name"=>"Pavla", "last_name"=>"Suchánková", "scopus_author_id"=>"24339282300"}, {"first_name"=>"Jaroslav", "last_name"=>"Doležel", "scopus_author_id"=>"7006010156"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84872825919", "sgr"=>"84872825919", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0054808", "pmid"=>"23372772", "pui"=>"368176513"}, "id"=>"0666faa9-e4e7-307b-b633-fac101c4cff5", "abstract"=>"Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.", "link"=>"http://www.mendeley.com/research/molecular-analysis-genomic-organization-major-dna-satellites-banana-musa-spp-3", "reader_count"=>19, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>12}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/503135"], "description"=>"*<p>International Transit Centre (<a href=\"http://www.bioversityinternational.org/research/conservation/genebanks/musa_international_transit_centre.html\" target=\"_blank\">http://www.bioversityinternational.org/research/conservation/genebanks/musa_international_transit_centre.html</a>).</p>", "links"=>[], "tags"=>["loci", "probes", "cl18", "cl33", "rrna", "genes", "bac", "clone", "2g17", "mitotic", "metaphase", "plates", "19", "accessions"], "article_id"=>173632, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.t003", "stats"=>{"downloads"=>6, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_loci_detected_using_FISH_with_probes_for_CL18_and_CL33_satellites_rRNA_genes_and_BAC_clone_2G17_on_mitotic_metaphase_plates_in_19_accessions_of_Musa_/173632", "title"=>"Number of loci detected using FISH with probes for CL18 and CL33 satellites, rRNA genes and BAC clone 2G17 on mitotic metaphase plates in 19 accessions of <i>Musa.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-23 01:00:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/503200"], "description"=>"a<p>Genome constitution as described in MGIS database (<a href=\"http://www.crop-diversity.org/banana/#AvailableITCAccessions\" target=\"_blank\">http://www.crop-diversity.org/banana/#AvailableITCAccessions</a>).</p>b<p>1 pg = 0.978×10<sup>9</sup> bp <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054808#pone.0054808-Doleel2\" target=\"_blank\">[34]</a>.</p>c<p>The study in which DNA content was estimated.</p>*<p>Estimated in the present work.</p>", "links"=>[], "tags"=>["accessions", "genome"], "article_id"=>173717, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_Musa_accessions_and_their_genome_sizes_/173717", "title"=>"List of <i>Musa</i> accessions and their genome sizes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-23 01:01:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/503167"], "description"=>"a<p>Primers used to prepare probes for FISH.</p>b<p>Primers were used to prepare probes for Southern hybridization.</p>", "links"=>[], "tags"=>["pcr", "amplification", "dna"], "article_id"=>173684, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_PCR_amplification_of_satellite_DNA_and_a_LINE_element_/173684", "title"=>"Primers used for PCR amplification of satellite DNA and a LINE element.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-23 01:01:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/503006"], "description"=>"<p>Chromosomes were counterstained with DAPI (blue). Sites of CL18 and CL33 probe hybridization are marked by long and thick arrows, respectively. (A) CL18 (red) and CL33 (green) on chromosomes of ‘Long Tavoy’. (B) 5S rDNA (red) and CL18 (green) on chromosomes of ‘Maia Oa’. (C) 5S rDNA (red) and CL33 (green) on chromosomes of ‘Long Tavoy’. (D) CL18 (red) and LINE element (green) on chromosomes of ‘Tuu Gia’. (E) 5S rDNA (red) and CL18 (green) on chromosomes of ‘Pisang Klutuk Wulung’. (F) BAC clone 2G17 (red) and 5S rDNA (green) on chromosomes of ‘Cameroun’. (G) BAC clone 2G17 (red) and CL18 (green) on chromosomes of ‘Tani’. (H) 45S rDNA (red) and 5S rDNA (green) on chromosomes of <i>M. schizocarpa</i> ITC 0560. (I) 5S rDNA (red) and CL33 (green) on chromosomes of <i>M. schizocarpa</i> ITC 1002. (J) CL18 (red) and CL33 (green) on chromosomes of <i>M. schizocarpa</i> ITC 1002. (K) CL18 (red) and 5S rDNA (green) on chromosomes of <i>M. schizocarpa</i> ITC 1002. Bar = 5 µm.</p>", "links"=>[], "tags"=>["genomic", "dna", "satellites", "mitotic", "metaphase", "chromosomes", "diploid", "accessions"], "article_id"=>173515, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_genomic_distribution_of_DNA_satellites_as_determined_on_mitotic_metaphase_chromosomes_of_diploid_Musa_accessions_after_FISH_/173515", "title"=>"Examples of genomic distribution of DNA satellites as determined on mitotic metaphase chromosomes of diploid <i>Musa</i> accessions after FISH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-23 00:58:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/502762"], "description"=>"<p>Samples of genomic DNA corresponding to 1×10<sup>7</sup> copies of monoploid (1C<sub>x</sub>) nuclear genomes were digested using <i>Dra</i>I restriction enzyme and hybridized with probes for CL18-like satellite (A) and CL33-like satellite (B) at hybridization stringency of 85%.</p>", "links"=>[], "tags"=>["hybridization", "genomic", "dna", "nineteen"], "article_id"=>173277, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Southern_hybridization_of_genomic_DNA_isolated_from_nineteen_Musa_accessions_/173277", "title"=>"Southern hybridization of genomic DNA isolated from nineteen <i>Musa</i> accessions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-23 00:54:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/502612"], "description"=>"<p>Consensus sequence of CL33-like satellite was reconstructed from all obtained sequence units of all analyzed accessions and is displayed as sequence logo (A). Neighbor-Joining tree constructed from a Jukes-Cantor distance matrix and rooted to the midpoint shows diversity of individual types of CL33-like repetitive units obtained from all studied accessions (B).</p>", "links"=>[], "tags"=>["cl33-like"], "article_id"=>173134, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_of_CL33_like_satellite_sequence_/173134", "title"=>"Diversity of CL33-like satellite sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-23 00:52:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/477818", "https://ndownloader.figshare.com/files/477819", "https://ndownloader.figshare.com/files/477820", "https://ndownloader.figshare.com/files/477829", "https://ndownloader.figshare.com/files/477831", "https://ndownloader.figshare.com/files/477833", "https://ndownloader.figshare.com/files/477835", "https://ndownloader.figshare.com/files/477840"], "description"=>"<div><p>Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (<em>Musa</em> spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within <em>M. acuminata</em> (A genome) and inter-specific crosses between <em>M. acuminata</em> and <em>M. balbisiana</em> (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified <em>in silico</em>. Their genomic organization and molecular diversity was analyzed in a set of nineteen <em>Musa</em> accessions, including representatives of A, B and S (<em>M. schizocarpa</em>) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between <em>Musa</em> species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in <em>M. acuminata</em> and <em>M. balbisiana</em> which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on <em>Musa</em> satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in <em>Musa</em>.</p> </div>", "links"=>[], "tags"=>["molecular", "genomic", "dna", "satellites"], "article_id"=>154123, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0054808.s001", "https://dx.doi.org/10.1371/journal.pone.0054808.s002", "https://dx.doi.org/10.1371/journal.pone.0054808.s003", "https://dx.doi.org/10.1371/journal.pone.0054808.s004", "https://dx.doi.org/10.1371/journal.pone.0054808.s005", "https://dx.doi.org/10.1371/journal.pone.0054808.s006", "https://dx.doi.org/10.1371/journal.pone.0054808.s007", "https://dx.doi.org/10.1371/journal.pone.0054808.s008"], "stats"=>{"downloads"=>20, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Analysis_and_Genomic_Organization_of_Major_DNA_Satellites_in_Banana_Musa_spp__/154123", "title"=>"Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (<em>Musa</em> spp.)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-23 01:08:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/502444"], "description"=>"<p>Consensus sequences of both parts of CL18-like satellite were reconstructed from all analyzed accessions and are displayed as sequence logo (A: CL18-part1; C: CL18-part2). Neighbor-Joining trees constructed from a Jukes-Cantor distance matrix and rooted to the midpoint show diversity of reconstructed parts of CL18-like satellite units obtained from all studied species (B: CL18-part1; D: CL18-part2).</p>", "links"=>[], "tags"=>["parts", "cl18-like"], "article_id"=>172965, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_diversity_of_the_two_parts_of_CL18_like_satellite_sequences_/172965", "title"=>"Sequence diversity of the two parts of CL18-like satellite sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-23 00:49:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/502910"], "description"=>"<p>(A) <i>M. acuminata</i> ‘DH Pahang’ ITC 1511; (B) <i>M. balbisiana</i> ‘Pisang Klutuk Wulung’; (C) <i>M. schizocarpa</i> ITC 0560.</p>", "links"=>[], "tags"=>["diploid"], "article_id"=>173427, "categories"=>["Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Jana Čížková", "Eva Hřibová", "Lenka Humplíková", "Pavla Christelová", "Pavla Suchánková", "Jaroslav Doležel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054808.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Idiograms_of_three_diploid_Musa_accessions_/173427", "title"=>"Idiograms of three diploid <i>Musa</i> accessions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-23 00:57:07"}

PMC Usage Stats | Further Information

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Relative Metric

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