Genome sequencing of Chlorella sp. A99, the symbiotic algae in hydra
Green hydra harbors symbiotic Chlorella in the endodermal epithelial cells. They established mutualistic relationship. The algae provides photosynthesis products to hydra, in return hydra gives nutrition including nitrogenous amino acids to the Chlorella. To understand interactions and evolution in the hydra-Chlorella symbiosis, genome sequence of the symbiont Chlorella sp. strain A99 was decoded.
For genome sequencing, Chlorella sp. A99 was isolated from green hydra H. viridissima A99 and the genomic DNA was extracted. Paired-end library (insert size: 740 bp) and mate-pair libraries (insert size: 2.2 and 15.2kb) were made using Illumina TruSeq DNA LT Sample Prep Kit and Nextera Mate Pair Sample Preparation Kit respectively. Genome sequencing was performed using Illumina Miseq and Hiseq 2000 platforms. Sequences reads were assembled by Newbler Assembler version 2.8 and subsequent scaffolding of the Newbler contigs was performed by SSPACE. Gaps inside the scaffolds were closed with the paired-end and mate-pair data using GapCloser of Short Oligonucleotide Analysis Package. In total, 17Gb data of the genome of Chlorella sp. A99 was sequenced to approximately 211-fold coverage, enabling the generation of an assembly comprising a total of 40.9 Mbp (82 scaffolds, N50=1.7Mbp). In Chlorella sp. A99 genome, 8298 gene models were predicted were predicted by AUGUSTUS.