You can vertically contatenate all of you data into a single column and use a [n x 2] grouping variable 'group' where group(:,1) identifies the G1, G2, G3 groups and group(:,2) identifies the column1 and column2 groups. Note that these groupings are also indicated in the x tick labels.
G1 = rand(108,2)-.5+[0,1];
G2 = rand(293,2)-.5+[2,4];
G3 = rand(30,2)-.5+[3,6];
group = [repelem([1;2;3],[numel(G1),numel(G2),numel(G3)]), ...
[repelem([1;2],size(G1,1));repelem([1;2],size(G2,1));repelem([1;2],size(G3,1))]];
boxplot([G1(:);G2(:);G3(:)],group)
