High-Quality Draft Genome Sequence of the Green Alga Tetraselmis striata (Chlorophyta) Generated from PacBio Sequencing.

A high-quality draft genome sequence of the microalgal species Tetraselmis striata was generated using PacBio sequencing. The assembled genome is 228 Mb, derived from 3,613 polished contigs at 84× coverage depth. This genome contains an average GC content of 57.9% and 48,906 predicted genes.

ANNOUNCEMENT

Photosynthetic eukaryotic microalgae sequester carbon into biomolecules that can be used for alternative sources of biomass and bioenergy. There is concerted effort among researchers from government, academia, and industry to identify and characterize algal species with desired feedstock phenotypes. Tetraselmis species comprise a genus of large, unicellular green algae that have great biofuel potential due to their adaptability to variable environmental conditions (1), symbiotic relationships with an extensive phycosphere (2), and ability to sequester carbon into lipids under stress (3). These marine algae are approximately 6 to 10 μm in diameter and covered in theca (sugar acid scales), with four flagella for motility (4, 5). Here, we report the first genome from the species Tetraselmis striata (formerly Platymonas).

Nannochloropsis salina CCMP1776 was grown in outdoor production ponds in southwestern Colorado (6). Samples collected from these ponds were cultured in vitro, and mixed algal species were noted. Tetraselmis striata was isolated from the N. salina culture using flow cytometry via size exclusion (10 μm versus 2 μm, respectively). T. striata was cultivated in modified f/2 medium (8.8 mM sodium nitrate) in 1-liter spin flasks and maintained at 25°C with 800 μmol · m−2 · s−1 fluorescent lighting on a 16h/8h light/dark cycle (7). Genomic DNA was extracted using agarose plugs and subsequently fragmented and purified to an average size of 20 to 40 kb for long-read sequencing. One PacBio SMRTbell library was generated. Eighteen single-molecule real-time (SMRT) cells were sequenced on the PacBio RS II platform using MagBead loading and C4 chemistry, and two SMRT cells were sequenced on the PacBio Sequel system using diffusion loading and C2 chemistry. De novo assembly was completed using Fast Alignment and CONsensus (FALCON) on sequencing data derived from the 20 SMRT cells (NCBI SRA accession no. SRR10043439 to SRR10043457). Based on previous transcriptomic data, the input genome size was set to 300 Mb, and seed coverage was set to 55×. There were 4,009,867 filtered subreads with a filtered subread length (N50) of 10,277. Default parameters were used to clean and filter the data. The FALCON assembly was polished twice using ReSequencing via SMRT Link v5.0.0 and corrected by PILON v1.22 using Illumina reads (NCBI SRA accession no. SRR10043458); both tools were run under default parameters. The final assembled genome contains 227,954,216 bases derived from 3,613 contigs, ranging from 710 to 4,140,848, with a GC content of 57.9% and an N50 value of 126,807 bp. The resulting assembly was annotated using BRAKER v2.0 with the default parameters specified for transcriptome sequencing (RNA-seq)-based training. The Tetraselmis sp. RNA-seq data used for training is located in the NCBI SRA database (accession no. SRR1296733 from the The Marine Microbial Eukaryote Transcriptome Sequencing Project) (8). Annotation generated 48,906 predicted gene models.

Data availability.

The annotated genome sequence is publicly available in the Greenhouse Knowledgebase at Los Alamos National Laboratory (https://greenhouse.lanl.gov/greenhouse) under “Algal Genomes: Tetraselmis striata” (https://greenhouse.lanl.gov/greenhouse/organisms/). This project has been deposited in GenBank under BioProject no. PRJNA542153, with the genome assembly deposited under accession no. VCJN00000000. The version described in this paper is the first version, VCJN01000000.