Thesis

Genome Assembly and Annotation of Isochrysis Galbana

Isochrysis Galbana is a species of cocoolithophores, which is a main factor of forming ocean's interior and sediments, and influencing the global cycles of carbon and sulfur. However, compared to its sister species Gephyrocapse Oceanica and Emiliania Huxleyi, Isochrysis Galbana has a different phenotype that it does not cause calcification sedimentation. In order to identify the genes and proteins involved in calcification that are presented in Emiliania Huxleyi and Gephyrocapse Oceanica but not in Isochrysis Galbana, the genome of Isochrysis Galbana was sequenced using Next-Generation Sequencing (NGS) technology.
 6,525Mb high quality sequence data from Illumina Solexa-Pipeline (HiSeq 2000) was assembled to estimated 84.30Mb genome of Isochrysis Galbana. The sequences were assembled into scaffolds by different assembling tools including Velvet extended by SSPACE, ABySS and ALLPATHS-LG. The best assembly result has 1,140 scaffolds and 419,869bp N50 scaffold length, with total genome length of 84,296,971bp. The assembly then was structural annotated by MAKER and PASA, and functional annotated by Blast2Go. As a result, the structural annotated genome includes 345 scaffolds with total length of 80,960,099bp. The genome has 36,670 exons, 35,608 CDS and 10,687 genes with total gene length of 24,150,153bp. From the functional annotation result, 5,150 out of 11,636 sequences have been found similarities with Emiliania Huxleyi, which verified Isochrysis Galbana is a sister species with Emiliania Huxleyi in cocoolithophores.

Isochrysis Galbana is a species of cocoolithophores, which is a main factor of forming ocean's interior and sediments, and influencing the global cycles of carbon and sulfur. However, compared to its sister species Gephyrocapse Oceanica and Emiliania Huxleyi, Isochrysis Galbana has a different phenotype that it does not cause calcification sedimentation. In order to identify the genes and proteins involved in calcification that are presented in Emiliania Huxleyi and Gephyrocapse Oceanica but not in Isochrysis Galbana, the genome of Isochrysis Galbana was sequenced using Next-Generation Sequencing (NGS) technology. 6,525Mb high quality sequence data from Illumina Solexa-Pipeline (HiSeq 2000) was assembled to estimated 84.30Mb genome of Isochrysis Galbana. The sequences were assembled into scaffolds by different assembling tools including Velvet extended by SSPACE, ABySS and ALLPATHS-LG. The best assembly result has 1,140 scaffolds and 419,869bp N50 scaffold length, with total genome length of 84,296,971bp. The assembly then was structural annotated by MAKER and PASA, and functional annotated by Blast2Go. As a result, the structural annotated genome includes 345 scaffolds with total length of 80,960,099bp. The genome has 36,670 exons, 35,608 CDS and 10,687 genes with total gene length of 24,150,153bp. From the functional annotation result, 5,150 out of 11,636 sequences have been found similarities with Emiliania Huxleyi, which verified Isochrysis Galbana is a sister species with Emiliania Huxleyi in cocoolithophores.

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