In the present study, we analyzed 5,535 BESs of two genomic BAC libraries of P. equestris, focusing on simple sequence repeat (SSR) or microsatellite content, repeat element composition, GC content, and protein-encoding regions.
GC content, repeat distribution and gene density in a 1-Mb sliding window are shown at 100-kb intervals.
Even though considerable genetic synteny was found in comparisons of other cereals to rice, sequencing of orthologous genomic regions uncovered considerable variation, in gene content, repeat structure and size.
The percent GC base composition (GC%), total repeat content (Repeats), LINE repeat content (LINEs), SINE repeat content (SINEs), LTR repeat content (LTRs), and other repeat types (Other) are shown for the ~721-kb musculus and ~717-kb spretus sequences encompassing the V1Ra/V1Rb gene cluster.
SSRs with low GC content from both libraries were significantly more allele-rich than high GC content repeat motifs.
Prior to the assembly, the quality of the sequencing data, overall GC content, repeat abundance or the proportion of duplicated reads should be assessed.
Before sequencing, bioinformatics analysis were carried out; the reference genome of cucumber was analyzed, considering the information on genomic GC content, repeat conditions, and genetic characteristics.
The well-assembled reference genome of mei was analysed beforehand, considering the information on genomic GC content, repeat conditions and genetic characteristics.
We focus all our analyses throughout this study between these two sets of chromosomes of a similar size, because microchromosomes have very different genomic features (i.e., recombination rate, gene density, GC content, repeat content etc).
To keep runtimes short, we prepared the target genome based on human chromosome 20, which accounts for 2%% of the human genome but has a reasonably representative GC content, repeat content and gene density compared with the whole genome.
