The word polyphiloprogenitive overwhelms everything in its vicinity and brings readers to a stop, from which they may find it difficult to get restarted. It's quite natural in such a situation for humble readers to blame themselves for lacking the necessary familiarity with the intimidating term to come to grips with the rest of the passage. But such self-blame is not always justified.
According to Merriam-Webster's Online Dictionary, polyphiloprogenitive (which has been around since at least 1919) has a single, simple definition: "extremely prolific." Let's try replacing the intimidating word in the sentence with its less scary definition (and include the preceding sentence in the article for context), and then see how it looks:
But we knew from the start the genome project would never be complete. The maps, or the sequences, are just the start of many lines of research, extremely prolific, multiply multiple genome projects.
To my mind, the second sentence of the excerpt is very nearly gibberish—an especially unfortunate circumstance given that it appears in a column that takes scientists to task for using "sloppy language" and for failing "to get more fully and precisely into the proper language of genetics." To make the OP's quotation coherent, you'd have to alter its back end extensively, along these lines:
But we knew from the outset that the genome project would never be complete. The maps, or the sequences, are just the start of many lines of research, as the progeny of this extremely prolific source of research opportunities will quickly multiply in the form of multiple subsidiary genome projects.
Considering that this article was published on 15 February 2001, I thought that perhaps the author's wording got garbled at some point after print publication, as sometimes happens to online articles when a Website changes its formatting and source code as part of a major site redesign (as must surely have occurred at Nature.com more than once in the 14 years since this article first appeared). But I haven't been able to find any online evidence that this happened, and I don't have access to a print copy of the relevant issue of Nature to check the original.
As to the OP's question about whether the quoted sentence makes sense as written, I don't think it does. Sometimes an emperor who looks naked to the unsophisticated eye really is naked.