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First, we scanned and identified the short reads in the metagenomic sequencing data that map to the human genome. By combining these reads across body sites (primarily originating from nares and cheek swabs [ 33 ]) for each individual (Additional file 1 : Figure S1), we attained a mean depth of coverage of more than 10 reads per base pair per individual (Additional file 1 : Figure S2).
Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F 1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem).
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