Comparative Genomic Analysis of Cryptophyte Algae Plastid Genomes

Cryptophyte algae have four different genomes. Through secondary endosymbiosis, cryptophytes derived the nuclear and mitochondrial genomes from an unknown eukaryote host and the nucleomorph and plastid genomes from a red algal. Cryptophytes are also important for studying photosynthesis. They have undergone differential retention and loss of photosynthetic genes due to some species being photosynthetic while others are non-photosynthetic. In collaboration with the Department of Energy (DOE) Joint Genome Institute (JGI), we sequenced the plastid genomes of 28 cryptophyte species and assembled them using NOVOPlasty. The assembled genomes were comprised of 1 - 7 contigs with 3 being the most common number. We used NCBI BLAST to align the contigs to reference genomes. For the majority of species, two contigs were found to align to the whole genome and rest of the contigs were hypothesized to be inverted repeats. Fourteen species were found to have a complete genome and hence they were qualified for downstream comparative genomic analyses. The sequencing depth was determined using Bowtie 2 and the results were visualized using Tablet. Average coverage depth ranged from 515 to 11,891, hence all 14 genomes had extremely good coverage depth. GeSeq was used for gene annotation. The GenBank files outputted by GeSeq were uploaded to GeneCo to visualize synteny and the presence/absence of genes among 8 published cryptophyte plastid genomes and 14 novel genome sequences presented here.