Novák, P., Hřibová, E., Neumann, P., Koblížková, A., Doležel, J., Macas, J.
PLoS ONE
9(6):
e98918,
2014
Keywords:
Abstract:
Background: 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.
Results: 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 interspecific
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.
Conclusions: 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.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Eva Hřibová
Čeština
English