Agave is both the scientific genus name and the common English name of the organism (which happens a lot). If it's used in a scientific context (such as a paper) you'd capitalize (the scientific name). In an article for people outside of the field you'd use lowercase (the common name).

Another example would be Boa constrictor. It's common name is the same, but lower case. So a newspaper article uses lower case, a herpetologist upper cases the Boa.