First draft of an annotated genome for a lichenised strain of the green alga Diplosphaera chodatii (Prasiolales, Trebouxiophyceae)

Although genome sequences of lichenized fungi are increasingly becoming available, genome sequences of microalgae involved in the lichen symbiosis are still scarce. For lichenized eukaryotic algae, genome sequencing has focused mostly on Trebouxia and Asterochloris, with little genomic data available for Stichococcus-like algae, such as Diplosphaera. The genus Diplosphaera is a common component of biological soil crusts, and often occurs associated with lichens of the family Verrucariaceae. It is characterized by cylindrical to spherical cells containing a plate-like chloroplast, and more specifically by a vegetative cell division that leads to the formation of typical two- to four-celled clusters. Here, we present a draft genome sequence for the algal partner of an Australian lichen specimen of Endocarpon pusillum. The genome was sequenced with Pac Bio long read and Illumina short read technologies, and transcriptome data were generated to inform the structural annotations. This algal strain is here identified as Diplosphaera chodatii based on nuSSU and ITS data. Compared with closely related lichenized and non-lichenized algae, the genome of D. chodatii stands out for its large size (85.6 Mb) and gene content (21,261 protein-encoding regions), as well as its high rate of duplicated genes (60% of the BUSCO genes are duplicated). These results suggest that whole genome duplication or large-scale segmental duplications may have occurred in the evolutionary history of this algal species. Little genome data are available for lichenized algae.We generated the first genome for a lichenized Diplosphaera chodatii.Results suggest a possible whole genome duplication in this species. Little genome data are available for lichenized algae. We generated the first genome for a lichenized Diplosphaera chodatii. Results suggest a possible whole genome duplication in this species.

尽管地衣化真菌（lichenized fungi）的基因组序列日益增多，但参与地衣共生（lichen symbiosis）的微藻（microalgae）基因组序列仍然十分匮乏。对于地衣化真核藻类而言，基因组测序主要集中于共球藻属（Trebouxia）和星孔藻属（Asterochloris），而对于双胞藻属（Diplosphaera）这类似织丝藻属（Stichococcus）藻类的基因组数据仍极为有限。双胞藻属是生物土壤结皮（biological soil crusts）的常见组分，常与疣壳菌科（Verrucariaceae）的地衣共生。该属的特征为细胞呈圆柱形至球形，内含板状叶绿体（chloroplast），更显著的是其营养细胞分裂（vegetative cell division）会形成典型的2至4细胞簇。本研究报道了澳大利亚薄囊地衣（Endocarpon pusillum）标本中藻类共生伙伴的基因组草图序列（draft genome sequence）。该基因组通过Pac Bio长读长测序与Illumina短读长测序技术完成组装，并结合转录组数据（transcriptome data）辅助进行结构注释（structural annotations）。基于核小亚基核糖体RNA（nuSSU）与内转录间隔区（ITS）序列数据，本研究将该藻类菌株鉴定为Chodat双胞藻（Diplosphaera chodatii）。与近缘的地衣化及非地衣化藻类相比，Chodat双胞藻的基因组以其庞大的基因组大小（85.6 Mb）、基因含量（21,261个蛋白质编码区域）以及极高的重复基因比例（60%的BUSCO基因（BUSCO genes）发生重复）而独具特色。上述结果表明，该藻类物种在演化历史中可能发生过全基因组复制（whole genome duplication）或大规模片段重复（segmental duplications）事件。目前地衣化藻类的基因组数据仍较为匮乏。本研究首次获得了地衣化Chodat双胞藻（Diplosphaera chodatii）的基因组序列。研究结果提示该物种可能存在全基因组复制事件。目前地衣化藻类的基因组数据仍较为匮乏。本研究首次获得了地衣化Chodat双胞藻（Diplosphaera chodatii）的基因组序列。研究结果提示该物种可能存在全基因组复制事件。