Repeats

Transposable element content was predicted for both de novo genomes and compared to the existing G. raimondii reference sequence (Paterson 2012). As expected, the de novo G. raimondii genome had nearly identical predicted TE content with the G. raimondii Paterson genome (Table XX_TE), with a difference of +2.1 Mb in the G. raimondii Paterson sequence. This difference is not significant and can be attributed to slight differences in assembly of repetitive regions. Consistent with the larger size of G. turneri (910 Mbp versus 880 Mbp in G. raimondii), the G. turneri genome assembled an additional 8.5 to 10.6 Mbp of repetitive sequence, relative to the Paterson and de novo G. raimondii sequences, respectively. Generally, the G. turneri genome has slightly fewer DNA TEs and more LTR retrotransposons than the two G. raimondii genomes, both with respect to absolute content and percent of genome (Table XX_TE). No non-LTR retrotransposons (e.g., LINE/SINE) were detected. For all three genome assemblies, retrotransposons comprise approximately 36% of the genome sequence, whereas all DNA elements combined comprise just under 3% in each. These results are consistent with genome skimming results for these two genomes (Grover et al, 2018).