Green algae of the phylum Chlorophyta are the most widespread autotrophic picoplankton in Lake Baikal (Russia). To expand our molecular biological knowledge of these microalgae and compare them in the future with an endosymbiotic strain, we present here the draft genome sequence of Chlorella sp. strain BAC9706.
ABSTRACT
Green algae of the phylum Chlorophyta are the most widespread autotrophic picoplankton in Lake Baika (Russia). To expand our molecular biological knowledge of these microalgae and compare them in the future with an endosymbiotic strain, we present here the draft genome sequence of Chlorella sp. strain BAC9706.
ANNOUNCEMENT
Green algae of the phylum Chlorophyta are the most widespread autotrophic picoplankton in Lake Baikal (Russia) (1 – 3). The related algae are symbionts of freshwater sponges and were assigned to the genus Choricystis based on analysis of the 18S rRNA and rbcL genes (4, 5). To expand our molecular biological knowledge of these microalgae and compare them in the future with an endosymbiotic strain, we present a draft version of the genome sequence of the Baikal autotrophic picoplankton green alga Chlorella sp. strain BAC9706.
Water samples containing microalgae were collected from the pelagic zone in the southern part of Lake Baikal, 5 km from Listvyanka (51.47°38′N, 104.55°54′E). The pure strain was obtained by serial transfers on BG-11 medium-enriched agar plates. Individual colonies of algae were cultivated in f/2 medium in 0.5-liter spin flasks, under constant illumination (200 μE m−2 s−1 white fluorescent light). The dense culture was harvested by centrifugation (300 × g, 15 min); the pellet was rapidly transferred and stored at −80°C until DNA isolation. In this study, genomic DNA of the green microalga Chlorella sp. strain BAC9706 was extracted from microalgal cultures using the Xpert directXtract plant lysis kit (GRiSP, Portugal).
Whole-genome sequencing was performed using the MiSeq platform with paired-end chemistry (2 × 250 bp) (Illumina, USA). A DNA library was prepared from genomic DNA using a Nextera DNA Flex library prep kit (Illumina). A total of 12,987,796 paired-end reads was obtained, giving a coverage depth of 60×. The hypervariable region of the 18S rRNA gene sequence was assembled with GetOrganelle v. 1.6.2e (6) (with default settings). Strain BAC9706 showed the highest 18S rRNA gene phylogenetic affiliation to species of the phylum Chlorophyta belonging to the genus Chlorella.
A draft assembly was built using SPAdes v. 3.13.0 with default settings, raw read filtering, and error correction with a built-in BayesHammer module (quality threshold, 98%) (7). This draft assembly contained 5,837 contigs with an N 50 value of 44,654 bp, and the largest contig was 317,606 bp long.
The resulting contigs were combined into scaffolds using Ragout v. 2.3 with default settings (https://github.com/fenderglass/Ragout) (8) using Chlorella vulgaris strain UTEX259 (GenBank accession no. VATW01000000) and Chlorella vulgaris strain UTEX 395 (GenBank accession no. LDKB01000000) as the reference genomes. We selected these two genomes from all the whole-genome sequences of Chlorella strains available in GenBank because the highest percentages of raw reads were mapped onto these genomes using Bowtie.
The final genome assembly had a total length of 32,957,766 bp, resulting in 201 scaffolds (N 50, 521,038 bp; L 50, 20), with a GC content of 61.92%; the largest scaffold was 1,817,640 bp.
Genome completeness analysis with BUSCO v. 3.1.0 using the “chlorophyta_odb10” data set with 2,168 benchmarking universal single-copy orthologs (BUSCOs) and default settings (9) showed results of 79.2% complete, 4.8% fragmented, and 16% missing. For the genome sequences of UTEX259 and UTEX 395, used as references, BUSCO reported 88.4% and 79.3% complete BUSCOs, respectively.
The presented draft nuclear genome assembly of Chlorella sp. strain BAC9706 provides a strong basis for comparative genetic analyses and will help elucidate metabolic processes.
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. JABWAE000000000. The raw reads are available via BioProject no. PRJNA591660 and SRA no. SRX7258937.
ACKNOWLEDGMENTS
This material is based upon work supported by the Russian Foundation for Basic Research (RFBR) under grant no. 18-04-00224. Sample collection was carried out within the framework of basic budget funding no. 0345-2019-0002 (АААА-А16-116122110066-1). The bioinformatics data analysis was performed in part on the equipment of the Bioinformatics Shared Access Center at the Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (ICG SB RAS).
REFERENCES
- 1.Nagata T, Takai K, Kawanobe K, Kim D-S, Nakazato R, Guselnikova N, Bondarenko N, Mologawaya O, Kostrnova T, Drucker V, Satoh Y, Watanabe Y. 1994. Autotrophic picoplankton in southern Lake Baikal: abundance, growth and grazing mortality during summer. J Plankton Res 16:945–959. doi: 10.1093/plankt/16.8.945. [DOI] [Google Scholar]
- 2.Belykh OI, Semenova EA, Kuznedelov KD, Zaika EI, Guselnikova NE. 2000. A eukaryotic alga from picoplankton of Lake Baikal: morphology, ultrastructure and rDNA sequence data. Hydrobiologia 435:83–90. doi: 10.1023/A:1004056604534. [DOI] [Google Scholar]
- 3.Fietz S, Bleiß W, Hepperle D, Koppitz H, Krienitz L, Nicklisch A. 2005. First record of Nannochloropsis limnetica (Eustigmatophyceae) in the autotrophic picoplankton from Lake baikal. J Phycol 41:780–790. doi: 10.1111/j.0022-3646.2005.04198.x. [DOI] [Google Scholar]
- 4.Belykh OI, Ekaterina G, Sorokovikova T, Saphonova A, Tikhonova IV. 2006. Autotrophic picoplankton of Lake Baikal: composition, abundance and structure. Hydrobiologia 568:9–17. doi: 10.1007/s10750-006-0340-8. [DOI] [Google Scholar]
- 5.Kulakova NV, Kashin SA, Bukin YS. 2020. The genetic diversity and phylogeny of green microalgae in the genus Choricystis (Trebouxiophyceae, Chlorophyta) in Lake Baikal. Limnology (Tokyo) 21:15–24. doi: 10.1007/s10201-019-00587-x. [DOI] [Google Scholar]
- 6.Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21:241. doi: 10.1186/s13059-020-02154-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and minimetagenomes from chimeric MDA products. J Comput Biol 20:714–737. doi: 10.1089/cmb.2013.0084. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. 2018. Chromosome assembly of large and complex genomes using multiple references. Genome Res 28:1720–1732. doi: 10.1101/gr.236273.118. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Waterhouse RM, Seppey M, Simao FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548. doi: 10.1093/molbev/msx319. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. JABWAE000000000. The raw reads are available via BioProject no. PRJNA591660 and SRA no. SRX7258937.