How compare two de novo assembled transcriptomes of the same sample with different sequencing depth?

Question

[seta]

Hi everybody,

I got two sequencing dataset derived from sequencing of one sample with two different sequencing depth, actually, one dataset is composed of about 48 million PE reads, 100bp and another contains about 300 million PE reads, 100 bp. The sample is a non-model plant with genome size of about 660 Mb that has not been sequenced. I've done de novo transcriptome assembly with both dataset and evaluated them using some basic parameters. However, I want to know which assembly (in fact which dataset) is much informative in terms of biological concepts to do further analysis on it. Could you please help me how I can accurately compare them to select the best one? Thanks for your help