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MongoDB document store model is very appreciated by developpers. But it also has limitations where MySQL is simply better.
Using MongoDB in conjonction with MySQL is becoming a very comon architectural pattern.

Comparing MongoDB, MySQL, and TokuMX Data Layout 2013-07-22 Zardosht Kasheff
pt-query-digest for MongoDB profiler logs    2013-07-23 hingo
Schema Design in MongoDB vs Schema Design in MySQL  2013-08-01 S. Combaudon
TokuMX Fractal Tree(R) indexes, what are they?  2013-07-02 Zardosht Kasheff