California-based Synthetic Genomics (SGI) and the Asiatic Centre for Genome Technology Sdn Bhd (ACGT) announced the joint venture last year, with the aim of developing more high-yielding and disease-resistant crops.
Oil palms are tropical trees grown for their fruit which are used to process palm oil - a form of vegetable oil.
As well as being used an ingredient for food and cosmetics, companies have also started choosing the oil as a biofuel, in attempts to find greener alternative to conventional petrol and diesel.
"Unlocking the knowledge encoded in the genomes could further increase our understanding of these important crops, which could lead to substantially improved oil yield," said Tan Sri Lim Kok Thay, chief executive of Asiatic Development Berhad.
"With such enhanced productivity, growing oil palm and jatropha could be sustainable solution to fulfilling the world's need for a wide variety of products."
Palm oil production has received wide attention recently as environmental campaigners have argued its production has contributed to the destruction of Indonesian forests and peatlands, increasing greenhouse gas (GHG) emissions and damaging habitats for animals such as the orangutan.
This has mounted pressures on companies to achieve more sustainable palm oil production.
Oil palm genome The researchers sequenced a combination of two palm varieties - tenure and dura.
They produced seven-fold coverage of the plant's genome, and claimed this was the most comprehensive sequence and analysis of the genome.
They said the oil palm is approximately 1.8bn base pairs in size, which is about four times the size of the rice genome and two thirds the size of the genome for maize.
The two companies will continue their analysis of the genome, so it can use this as a reference genome.
The partners have announced progress in sequencing and analyzing the jatropha genome.
Jatropha is a robust oil seed crop that can be converted into clean, renewable fuels.
ACGT and CGI said the crop has significant potential for improving yield.
J Craig Venter, founder and CEO of SGI, said: "The genome sequences of these highly productive oilseed crops will enable the in-depth understanding of genes encoding for plant yield and health and foster the development of improved plant varieties.
We are also characterizing the important microbes living in the environments around these plants."
The partners said analyzing the root, soil and leaf as well as understanding the environments will help them to develop diagnostic tests for plant diseases and agents for their control, leading to healthier and more productive crops.
"Our goal is to harness this knowledge to produce improved feedstocks, renewable fuels, biofertilizers, and disease-control solutions," added Venter.
Environmental concerns ACGT's is owned by Asiatic Development Berhad, a plantation arm of the Genting Group, which is a member of the Roundtable on Sustainable Palm Oil (RSPO).
The RSPO is an international multi-stakeholder organization set up six years ago to promote the growth and use of sustainable palm oil through cooperation within the supply chain and open dialogue between its stakeholders.
Palm oil sustainability has been a great area of concern for environmental campaigners.
In November, Greenpeace produced a report saying major food companies, including Unilever, Nestle and Cargill, were contributing to increased carbon emissions through their use of palm oil, and such production could "trigger a climate bomb" .
Every year, 1.8bn tonnes of GHG emissions are released by the degradation and burning of Indonesia's peatlands, according to Greenpeace.
This is 4 percent of global GHG emissions, and comes from 0.1 percent of the land on earth.
In a recent follow-up report, the environmental charity presented further evidence of the expansion of the palm oil sector in Indonesia.
Furthermore, it linked the majority of the largest producers in Indonesia to Unilever, which uses 1.3 Mt of palm oil derivative each year, equal to about 3 percent of global production.
Unilever has since promised to ensure its sources are sustainable, to help protect the environment.