Coconut Genome de novo Sequencing

Coconut (Cocos nucifera) is a member of palm family (Arecaceae).  It is cultivated in more than 80 countries across the world. The coconut plant, including its fruit, is a source for a variety of valuable industrial products, such as coconut oil, coconut milk, coir and some beauty products. In this work, we try to produce a high quality draft of coconut genome. We built 7 libraries for pair-end and mate-pair genome sequencing using HiSeq. Our estimation for the coconut genome size is around 2.6 Gb, with repetitive sequences between 50 to 70 percent based on partial data analysis. We tried ALLPATHS-LG and SOAPdenovo2 for genome assembly using default parameters, but the results were unsatisfactory (N50 is 48kb, genome coverage is 37% and total gap is 26% for ALLPATHS-LG, and N50 is 67kb, genome coverage is almost 100% and total gap is 29% for SOAPdenovo2). The reason for poor assembly may be due to low genome coverage, high repeat content and lack of large insert size libraries.

Therefore, we devised our own assembly pipeline using some Soap assembly and gap closing modules, SSPACE scaffolder and intermediate correction scripts developed in-house. Our pipeline, produced significantly improved quality genome draft (N50 is 114kb, genome coverage is 94.5% and total gap is only 10%). We used raw library alignment (to each draft) results to verify that our pipeline doesn’t introduce undesired misassembly problems in addition to those resulting from standard pipelines.