The complete chloroplast genome of Isochrysis galbana and comparison with related haptophyte species

Abstract

The haptophyte Isochrysis galbana is an algal species of commercial interest due to its ability to accumulate high levels of fucoxanthin. In this study, the complete chloroplast (cp) genome of I. galbana was sequenced using a combination of Illumina and third-generation sequencing platforms. This circular cp genome was 105,872 bp in length, consisting of a large single-copy (LSC) region of 54,838 bp and a small single-copy (SSC) region of 41,308 bp separated by two direct rDNA repeats of 4862 bp and 4864 bp. The cp genome contained 141 unique genes, including 112 protein-coding genes with no introns, 26 transfer-RNA (tRNA) genes and three ribosomal-RNA (rRNA) genes. Like canonical ribosomal operon repeat structure, two 16S-trnI-trnA-23S-5S ribosomal RNA operons were identified. A total of 32 pairs of small repeats and 45 perfect microsatellites were detected. All haptophyte chloroplasts sequenced to date apart from E. huxleyi have either a complete pair of canonical repeats with direct orientation or noncanonical inverted repeats that lost part of tRNAs, or they have lost the inverted repeat arrangement altogether. Additionally, imperfect ribosomal operon repeats were observed in most haptophytes. The non-identical 4.9 kb ribosomal direct-repeats in I. galbana cp genome were distinguished by three 1–2 bp-sized inserts/deletions (InDels) and 32 single nucleotide polymorphisms (SNPs). Pairwise chloroplast genome comparisons showed a high degree of conservation in genome structure, gene order and gene content between I. galbana and T. lutea, with an overall SNP mutation rate of 4.3 × 10−3 per site. Only 458 SNPs, 18 small InDels and one large insertion were detected between these two cp genomes. The transition-to-transversion (Ts/Tv) ratio was 1.79 and the predominant mutations were A/T to G/C transitions. Phylogenetic analysis of currently available haptophyte chloroplasts also reflected that I. galbana was most closely related to T. lutea. The Ka/Ks ratios of shared genes in Isochrysidales chloroplast genomes were less than 1, suggesting that those genes are under purifying selection. The phylogenetic tree yielded by plastome single-copy orthologous genes gives new evidence on the relationships among CASH lineages. This first I. galbana chloroplast genome will provide insight into the chloroplast architecture, function and evolution of this species and other haptophytes.