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.

触藻等鞭藻是一种具有商业价值的藻类，因为它能够积聚高水平的岩藻黄质。在这项研究中，I。galbana的完整叶绿体（cp）基因组使用Illumina和第三代测序平台进行测序。该环状cp基因组的长度为105,872 bp，由54,838 bp的大单拷贝（LSC）区和41,308 bp的小单拷贝（SSC）区组成，由两个分别为4862 bp和4864 bp的直接rDNA重复序列隔开。cp基因组包含141个独特基因，包括112个无内含子的蛋白质编码基因，26个转移RNA（tRNA）基因和3个核糖体RNA（rRNA）基因。像典型的核糖体操纵子重复结构一样，鉴定了两个16S-trnI-trnA-23S-5S核糖体RNA操纵子。总共检测到32对小重复序列和45个完美的微卫星。除狐E外，迄今已对所有触藻植物叶绿体进行了测序具有完整的一对直接定向的经典重复序列或丢失了部分tRNA的非经典反向重复序列，或者它们完全失去了反向重复序列排列。另外，在大多数触藻中观察到不完善的核糖体操纵子重复序列。gal.ana cp基因组中不同的4.9 kb核糖体直接重复序列以三个1–2 bp大小的插入/缺失（InDels）和32个单核苷酸多态性（SNP）区分。成对叶绿体基因组比较显示，I。galbana和T. lutea之间的基因组结构，基因顺序和基因含量高度保守，总SNP突变率为4.3×10 ^-3每个站点。在这两个cp基因组之间仅检测到458个SNP，18个小InDel和一个大插入。转换至转换（Ts / Tv）的比率为1.79，主要突变为A / T至G / C转换。对目前可获得的触生叶绿体进行的系统发育分析也反映了I. galbana与T. lutea关系最为密切。鞘翅目叶绿体基因组共享基因的Ka / Ks比小于1，表明这些基因正在纯化选择中。质体组单拷贝直系同源基因产生的系统树为CASH谱系之间的关系提供了新的证据。第一个加尔各答 叶绿体基因组将提供有关该物种和其他触藻的叶绿体结构，功能和进化的见解。