Amyris Biotechnologies has raised $41.75 million as part of a C round to fund the commercialization of the company's biofuel and chemicals in 2011.

The Emeryville, Calif.-based startup began raising the round this summer, and it aims to raise "approximately $60 million."

Amyris was able to raise the first, $24.7 million by August (the date of first sale was July 31), according to its filing with the U.S. Securities and Exchange Commission. The filing said the company was seeking to raise $62 million.

New investors for the round included GrupoCornelioBrennand in Brazil and Naxos in the United Kingdom, Amyris said. Earlier investors Khosla Ventures, Kleiner Perkins Caufield & Byers, TPG Biotech and Votorantim Novos Negocios also put in money this time.

If Amyris successfully closes a C round of $60 million, then it will have raised a total of about $165 million in equity since its inception in 2003, the company said in a press release Thursday. However, a company's press release in June this year said it already had raised "over $125 million in equity funding." We have put in a call to ask for clarification. UPDATE: Amyris's spokeswoman Casondra Prince said the $165 million would actually only count the $41.75 million raised for the C round so far, not the entire $60 million the company expects to raise to complete the C round.

Amyris has engineered yeast that ingest sugar and secrete hydrocarbon, a method that involves fewer steps and possibly cheaper than what its competitors have been able to achieve.

The company opened a pilot production plant at its headquarters last November, when CEO John Melo touted the startup's ability to produce a form of diesel that it could sell for $2 per gallon or less. That was about how much conventional fossil diesel would cost (see Amyris: Were Better Than Biodiesel, Ethanol or Gas).

In June this year, Amyris opened a demonstration plant in Brazil to take advantage of the abundant sugarcane supply as feedstock.

The company also is developing jet fuel and chemicals that could replace those that rely on petroleum as the raw material.

Amyris hopes to build commercial plants and sell its fuels and chemicals from those facilities starting in 2011. The company is working on finding a suitable site for its commercial project, and plans to order equipment for the plant by the end of this year.

The path to producing biofuels typically involves two processes: converting plants or some sort of biomass into sugar, and then feed the sugar to microbes, algae or other organisms for fuel making.

The second process typically yields lipids or chemical compounds that require further refining to become commercial products.

Amyris' yeast skips that refining step and secretes hydrocarbon as a direct hydrocarbon replacement. Its key competitors include Mascoma in Lebanon, N.H., and LS9 in South San Francisco, both companies also claim to have devised a simpler and more cost effective way to produce fuels.

Some startups have opted to skip the use of sugar altogether. Joule Biotechnologies in Cambridge, Mass., emerged from stealth mode last month to provide a glimpse of its technology.

Joule has developed organisms that thrive under sunlight and in tanks filled with carbon dioxide, and they could secrete hydrocarbon or ethanol (see Joule Biotech: Does It Have the Superbug for Biofuel?). One of Joule's founders, David Berry of Flagship Ventures also co-founded LS9.

Tags: amyris, geva, joule biotechnologies, ls9, mascoma