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Nipponbare remains as the only monocot genome that has been sequenced to a high-quality level.

The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level.

Although most of these genomes have been sequenced to a very low coverage (1.25×), each sub-group was detected in almost all genomes.

The genomes of Gallus gallus and Taeniopygia guttata have been sequenced to a 6.6 X coverage and a 5.5 X coverage respectfully [ 7, 32].

In addition, utilizing 454 sequencing technology, the entire T. aestivum genome has been sequenced to a 5× coverage; from which several low copy number sequences and gene models based on orthologous sequences from other grass species were proposed [ 15].

However, due to the wide success of AM in nature, non-mycorrhizal species are the exception (estimated 10-20% of the angiosperm species), and only few of them have been sequenced to a degree that they could be used for such an approach.

Samples were sequenced to an average depth of 36 million reads (Supplementary Table S1), and blanks were sequenced to a depth of 0.4 1 million reads (Supplementary Table S10).

Samples were sequenced to a depth of approximately 5 million reads per library (Supplementary Table S1), and blanks were sequenced to a depth of 157,109 to 841,776 reads (Supplementary Table S10).

All RNA-seq was sequenced to a depth of 50 M tags, and 150 bp paired-end.

Each whole-genome DNA library was sequenced on the HiSeq platform (Illumina) to a mean coverage of 15x and each whole-exome library was sequenced to a mean coverage of 80x.

The paired-end DNA libraries had an average insert size of ~ 500 bp and were sequenced to a depth of 14-fold genome coverage20, which allowed clear distinction between mPing, Ping, and Pong elements (Fig. 1a).