Genome-wide analysis of repeat diversity across the family Musaceae.

TitleGenome-wide analysis of repeat diversity across the family Musaceae.
Publication TypeJournal Article
Year of Publication2014
AuthorsNovák P, Hřibová E, Neumann P, Koblížková A, Doležel J, Macas J
JournalPLoS One
Volume9
Issue6
Paginatione98918
Date Published2014
ISSN1932-6203
KeywordsComputational Biology, DNA, Plant, Evolution, Molecular, Genetic Variation, Genome, Plant, Musaceae, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA
Abstract

<p><b>BACKGROUND: </b>The 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.</p><p><b>RESULTS: </b>Low-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.</p><p><b>CONCLUSIONS: </b>This 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.</p>

DOI10.1371/journal.pone.0098918
Alternate JournalPLoS ONE
PubMed ID24932725
PubMed Central IDPMC4059648
Showing 17 of 17 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Musa ornata ITC0370 ornata subsp. ornata Unknown ITC
Calcutta 4 ITC0249 acuminata subsp. burmannicoides India ITC
Musa mannii ITC1411 Unknown Unknown Unknown ITC
Musa beccarii ITC1070 beccarii subsp. beccarii Unknown ITC
Malaccensis ITC0250 acuminata subsp. malaccensis Unknown ITC
Tani ITC1120 balbisiana Unknown Unknown ITC
Musa coccinea ITC0287 coccinea subsp. coccinea Unknown ITC
Musa peekelii ssp. peekelii ITC0917 peekelii subsp. peekelii Papua New Guinea ITC
Honduras ITC0247 balbisiana Unknown Unknown ITC
Musa velutina ITC0011 velutina subsp. velutina Unknown ITC
Ensete gilletii
ITC1389 gilletii subsp. gilletii Unknown ITC
Musa maclayi type Hung Si
ITC0614 maclayi subsp. maclayi Papua New Guinea ITC
Kluai Bou
ITC0528 ornata subsp. ornata Unknown ITC
Musa ornata
ITC0637 ornata subsp. ornata Unknown ITC
Musa textilis
ITC0539 textilis subsp. textilis Unknown ITC
Ensete ventricosum
ITC1387 ventricosum subsp. ventricosum Unknown ITC
Maia Oa
ITC0728 acuminata subsp. zebrina Unknown ITC