Draft Genome Sequences of Four Species of Chlamydomonas Containing Phosphatidylcholine
ABSTRACT
Phosphatidylcholine (PC) is one of the essential phospholipids for most eukaryotes. Although the model green alga Chlamydomonas reinhardtii lacks PC, four species containing PC were found in the genus Chlamydomonas. Here, we report the draft genome sequences of the four species of Chlamydomonas containing PC.
GENOME ANNOUNCEMENT
Most eukaryotic organisms contain phosphatidylcholine (PC), but various algae, including a unicellular green alga, Chlamydomonas reinhardtii, are known to lack PC (1, 2). In these algae, the phosphorus-free betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) has been thought to function in place of PC (1, 2). In some nonphotosynthetic microorganisms possessing both PC and DGTS, phosphate starvation induced a decrease in PC and an increase in DGTS (3, 4). The apparent complete replacement of PC with DGTS in PC-lacking algae could be a result of adaptation to a phosphorus-limited environment.
We recently detected PC in four species of the genus Chlamydomonas: C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242 (5). PC biosynthetic pathways and the enzymes involved therein have been revealed in yeasts, mammals, and land plants (6) but remain unclear in most algae.
C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242, which were obtained from the Microbial Culture Collection at the National Institute for Environmental Studies, Japan, were grown photoautotrophically in modified Bristol's medium (7). Genomic DNA from each of these species was released by treatment with proteinase K and sodium N-dodecanoylsarcosinate and isolated by CsCl density gradient ultracentrifugation, as described previously (8). Purified DNA was submitted to paired-end sequencing by Illumina HiSeq 2000 (C. sphaeroides) or MiSeq (other three species) through the sequencing service of TaKaRa Bio, Inc. (Otsu, Japan). The obtained reads were assembled using the software Velvet version 1.2.08 (9).
The total length of draft genomes in C. sphaeroides and C. debaryana that are closely related to C. reinhardtii (10) was also close to the genome size of C. reinhardtii (around 120 Mbp) (11). The other two species had genomes that were smaller (79 Mbp, C. applanata) or larger (145 Mbp, C. asymmetrica) than that of C. reinhardtii, showing considerable variation in genome size within the genus Chlamydomonas.
Putative genes involved in the biosynthesis of PC were searched using the tblastn program (12). The three-step methylations of phosphatidylethanolamine and/or phosphoethanolamine are necessary for the de novo synthesis of PC, and they are catalyzed by phosphatidylethanolamine-N-methyltransferase (PEMT) and/or phosphoethanolamine-N-methyltransferase (PEAMT), respectively. All four species analyzed in the present study were found to harbor a single putative gene coding for PEMT, whereas a putative gene encoding PEAMT was found in C. applanata and C. asymmetrica only. These results suggest that at least two different types of pathways exist for the PC biosynthesis in these species. The draft genome sequences reported here, however, will be useful in finding not only lipid-related genes (13) but also genes involved in diverse cellular functions.
Accession number(s).
The draft genome sequences of the four Chlamydomonas species were deposited in DDBJ/EMBL/GenBank under the accession numbers listed in Table 1. The version described in this paper is the first version.
TABLE 1
| Species | Accession no. | Approximate genome size (Mbp) | No. of scaffolds (>1,000 bp) | Coverage (×) |
|---|---|---|---|---|
| C. applanata NIES-2202 | BDCZ00000000 | 79 | 2,533 | 21.4 |
| C. asymmetrica NIES-2207 | BDDA00000000 | 145 | 4,102 | 11.2 |
| C. debaryana NIES-2212 | BDDB00000000 | 126 | 10,139 | 10.5 |
| C. sphaeroides NIES-2242 | BDDC00000000 | 127 | 6,890 | 34.1 |
ACKNOWLEDGMENTS
We are grateful to Kenta Sakurai for initial help in the experiment.
This work was supported in part by a grant-in-aid for Core Research for Evolutional Science and Technology (CREST) from the Japan Science and Technology Agency.
REFERENCES
1.
Sato N, Furuya M. 1985. Distribution of diacylglyceryltrimethylhomoserine and phosphatidylcholine in non-vascular green plants. Plant Sci 38:81–85.
2.
Giroud C, Gerber A, Eichenberger W. 1988. Lipids of Chlamydomonas reinhardtii. Analysis of molecular species and intracellular site(s) of biosynthesis. Plant Cell Physiol 29:587–595.
3.
Geiger O, Röhrs V, Weissenmayer B, Finan TM, Thomas-Oates JE. 1999. The regulator gene phoB mediates phosphate stress-controlled synthesis of the membrane lipid diacylglyceryl-N,N,N-trimethylhomoserine in Rhizobium (Sinorhizobium) meliloti. Mol Microbiol 32:63–73.
4.
Riekhof WR, Naik S, Bertrand H, Benning C, Voelker DR. 2014. Phosphate starvation in fungi induces the replacement of phosphatidylcholine with the phosphorus-free betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine. Eukaryot Cell 13:749–757.
5.
Sakurai K, Mori N, Sato N. 2014. Detection and characterization of phosphatidylcholine in various strains of the genus Chlamydomonas (Volvocales, Chlorophyceae). J Plant Res 127:641–650.
6.
Lykidis A. 2007. Comparative genomics and evolution of eukaryotic phospholipid biosynthesis. Prog Lipid Res 46:171–199.
7.
Watanabe A. 1960. List of algal strains in collection at the Institute of Applied Microbiology, University of Tokyo. J Gen Appl Microbiol 6:283–292.
8.
Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S, Ikeuchi M, Sato N. 2011. Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S. DNA Res 18:393–399.
9.
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829.
10.
Yumoto K, Kasai F, Kawachi M. 2013. Taxonomic re-examination of Chlamydomonas strains maintained in the NIES-Collection. Microbiol Cult Coll 29:1–12.
11.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, et al. 2007. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245–250.
12.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic Local Alignment Search Tool. J Mol Biol 215:403–410.
13.
Sato N, Mori N, Hirashima T, Moriyama T. 2016. Diverse pathways of phosphatidylcholine biosynthesis in algae as estimated by labeling studies and genomic sequence analysis. Plant J 87:281–292.
Information & Contributors
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Published In
Genome Announcements
Volume 4 • Number 5 • 27 October 2016
eLocator: 10.1128/genomea.01070-16
Copyright
© 2016 Hirashima et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
History
Received: 7 August 2016
Accepted: 9 August 2016
Published online: 29 September 2016
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Citation
2016.
Draft Genome Sequences of Four Species of Chlamydomonas Containing Phosphatidylcholine. Genome Announc
4:10.1128/genomea.01070-16.
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