Based on the observation of such overlapping, we can easily detect the repeating locations by shifting and matching the whole target sequence without knowing the nucleotide contents of repeated patterns.
The quinoa genome has a high content of repeat sequences, making up 64.5% of the genome, more than half of which are retrotransposons.
The low content of repeat elements of only about 3.1% further facilitates the genome assembly.
For models with repeat features, the content of repeat families as well as individual repeats were extracted from UCSC annotations.
While global genomic re-sequencing remains overambitious given the large size of the wheat genome [ 35] along with the high content of repeat sequences (>80 %) [ 36], current DNA sequencing platforms are well capable of uncovering sequence variation in the transcriptome.
We verified that different amount and content of repeat elements, especially the different accumulation of transposable elements, are responsible for the genome size variation between D. holocanthus and smooth pufferfish.
Circos [ 58] was used for illustration of nuclear genome data such as: chromosome structure (position of centromeres, tRNA and rRNA genes), density of genes across the genome, content of repeat DNA, 454 reads mapped to chromosomes, syntenic blocks between A. adeninivorans and genomes of Y. lipolytica, K. pastoris and S. cerevisiae.
As a consequence, despite the good overall quality of the chicken draft assembly, which benefited from the relatively small content of repeat sequences, a large fraction corresponding to 10 of the smallest microchromosomes was missing in the first version of the published sequence assembly (February 2004) [ 6].
Due to the huge genome size of the hexaploid (17 Gbp) [ 1] along with the high content of repeat sequences, it is very difficult to carry out complete sequencing of the entire genome or to perform forward genetics in polyploid wheat.
Sequencing and annotation of the T. melanosporum genome, the first symbiotic Ascomycete to be sequenced, revealed many aspects of truffles' biology and genetic organization, including their massive content of repeated transposable elements and their heterotallic mode of conjugation and ability to outcross through the action of two distinct mating type loci (Martin et al. [2010]).
