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Metal Gear Solid: The Twin Snakes
Yoshi appears in Metal Gear Solid: The Twin Snakes as a cameo along with Mario in Dr. Emmerich's laboratory. If the player shoots Yoshi, he'll say his name. If the player shoots Mario, a "1-Up" sound can be heard and Solid Snake will gain a little bit of health.
Super Smash Bros. Brawl
Yoshi and Solid Snake both appear as characters in Super Smash Bros. Brawl. During a Codec conversation with Otacon, Snake says he's interested in catching Yoshi and eating him as food, to Otacon's disgust.
Metal Gear Solid: Snake Eater 3D
In Metal Gear Solid: Snake Eater 3D, Yoshi has replaced all the Kerotans, though many Yoshi locations have been rearranged from the original Kerotan hiding spots. When near Yoshi, the player will hear him making the same sound that he makes when sticking out his tongue. After shaking Yoshi, he also utters the cry he used in all of his appearances prior to Yoshi's Story. Para-Medic will also speculate that Yoshi was becoming popular to the Soviet Union if the player calls her upon discovering and/or shaking it. On a related note, the Kerotan rank was replaced with Yoshi, and Para-Medic instead talks about Yoshi when called about them.
Similarly, the GA-KO camouflage has been replaced with the Fruit Camo uniform. It performs the same functions as the GA-KO Camo did previously, just updated to reflect the overall change from Kerotan to Yoshi. The name and design of the uniform is a reference to certain items Yoshi can ingest in various Mario games, namely Super Mario World and Yoshi's Story.