Isolation and characterization of the highly repeated fraction of the banana genome

Hřibová, Eva; Doleželová, Marie; Town, Chris; Macas, Jiří; Doležel, Jaroslav

doi:10.1159/000112073

Cited by 22 publications

(30 citation statements)

References 75 publications

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“…At the same time, breeding of improved cultivars is hampered by seed sterility, unknown origin of the cultivated clones, and poor knowledge on genetic diversity of the genus Musa . The nuclear genome of Musa species is relatively small (1C∼600 Mbp; [16], [17]), and previous studies showed that ∼55% of the genome is represented by repetitive DNA, especially different types of retroelements [18]–[20]. Genomic repeats evolve more rapidly than coding sequences, and plant geneticists and breeders found them a unique source of molecular markers to map important genes, analyze genetic diversity, and study processes of speciation and genome evolution [21]–[23].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

et al. 2014

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BackgroundThe banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family.ResultsLow-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR) retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14–34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis) shared similar populations of repetitive elements.ConclusionsThis study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

et al. 2014

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“…It has been estimated that about 55% of the genome is made of various DNA repeats [5], but only a limited number of repetitive DNA sequences has been characterized. Valárik et al .…”

Section: Introductionmentioning

confidence: 99%

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

et al. 2010

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BackgroundBananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement.ResultsIn this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. 'Calcutta 4') genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones.ConclusionA low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic diversity studies and in marker-assisted selection.

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“…(Katsiotis et al, 1997), banana (Musa spp. ;H ribová et al, 2007), and other plant species (Sharma and Raina, 2005) because they tend to form clusters, which facilitates their detection and positive chromosome identification. In this study, 11 newly characterized satellites provided localized signals on one or more chromosomes of meadow fescue and could serve as new cytogenetic markers in this species and probably also in ryegrasses.…”

Section: Newly Identified Repeats Are a Valuable Source Of Cytogenetimentioning

confidence: 99%

Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

et al. 2013

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The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 503 coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.

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Isolation and characterization of the highly repeated fraction of the banana genome

Cited by 22 publications

References 75 publications

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

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