The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA.
BACKGROUND
Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of beta-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri.


RESULTS
The D. salina organelle genomes are large, circular-mapping molecules with approximately 60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: approximately 1.5 and approximately 0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA.


CONCLUSIONS
These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming D. salina nuclear genome sequence, placing D. salina in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.
Smith
David Roy
DR
Department of Biology, Dalhousie University, Halifax, Canada. smithdr@dal.ca
Lee
Robert W
RW
Cushman
John C
JC
Magnuson
Jon K
JK
Tran
Duc
D
Polle
Jürgen E W
JE
D000460:Chlorophyta / Q000235:genetics*; D002874:Chromosome Mapping; D048028:DNA, Algal / Q000235:genetics; D021901:DNA, Intergenic; D004272:DNA, Mitochondrial / Q000235:genetics; D023061:Gene Order; D054629:Genome, Mitochondrial; D054627:Genome, Plastid; D007438:Introns; D017422:Sequence Analysis, DNA
D048028:DNA, Algal; D021901:DNA, Intergenic; D004272:DNA, Mitochondrial
J Mol Evol. 1998 Oct;47(4):431-40
9767688
J Appl Microbiol. 2009 Jul;107(1):14-35
19245408
BMC Genomics. 2008 Jul 26;9:350
18655725
J Mol Evol. 2008 Dec;67(6):696-704
19018585
Trends Biotechnol. 2004 Jun;22(6):311-8
15158061
Trends Genet. 2007 Mar;23(3):119-25
17280737
J Phycol. 2009 Dec;45(6):1323-34
27032590
Mol Biol Evol. 1996 Jan;13(1):233-43
8583896
Philos Trans R Soc Lond B Biol Sci. 1988 May 31;319(1193):135-47
2901763
Mol Biol Evol. 2010 Oct;27(10):2244-56
20430860
Curr Genet. 1991 Apr;19(4):309-12
1831072
Plant Physiol. 2007 Dec;145(4):1129-43
18056863
Science. 1988 Jun 10;240(4858):1534-8
2897716
Adv Exp Med Biol. 2007;616:34-45
18161489
J Eukaryot Microbiol. 2006 Mar-Apr;53(2):79-84
16579809
J Ind Microbiol Biotechnol. 2009 Feb;36(2):269-74
18982369
Mol Cell Biol. 1994 Sep;14(9):6180-6
8065351
Nucleic Acids Res. 2008 Aug;36(14):4529-48
18587153
Am J Bot. 2004 Oct;91(10):1535-56
21652308
Mol Biol Evol. 1998 Jun;15(6):690-701
9615450
BMC Evol Biol. 2009 May 27;9:120
19473533
Plant Mol Biol. 1994 Feb;24(4):585-602
8155879
Mol Biol Evol. 2007 Jul;24(7):1528-36
17440175
Plant Cell. 2002 Nov;14(11):2659-79
12417694
Annu Rev Plant Biol. 2004;55:289-313
15377222
EMBO J. 1994 Feb 15;13(4):898-905
8112303
Nucleic Acids Res. 2003 Jan 1;31(1):439-41
12520045
Bioinformatics. 1999 May;15(5):426-7
10366664
BMC Genomics. 2009 Mar 26;10:132
19323823
Mol Genet Genomics. 2006 Nov;276(5):464-77
16944205
Bioinformatics. 2004 Jan 22;20(2):279-81
14734323
Plant Mol Biol. 1995 Jan;27(2):351-64
7888624
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337
Nucleic Acids Res. 1998 May 15;26(10):2286-90
9580676
BMC Evol Biol. 2008 May 21;8:156
18495022
Adv Exp Med Biol. 2007;616:90-8
18161493
Science. 2006 Mar 24;311(5768):1727-30
16556832
Mol Biol Rep. 2009 Jul;36(6):1433-9
18792804
Genetics. 2007 Feb;175(2):819-26
17151253
Mol Biol Evol. 2008 Mar;25(3):487-96
18222946
Curr Opin Biotechnol. 2008 Oct;19(5):430-6
18725295
Plant Physiol. 1995 Aug;108(4):1657-1664
12228570
Curr Genet. 1993 Sep;24(3):241-7
8221933
Plant Mol Biol. 1998 Jan;36(2):285-95
9484440
Mol Biol Evol. 2006 Nov;23(11):2175-90
16916942
Mol Biol Evol. 1997 May;14(5):506-17
9159928
Mol Biol Evol. 2002 Jul;19(7):999-1007
12082120
Mol Phylogenet Evol. 2008 Jul;48(1):281-91
18430591
Curr Genet. 2004 May;45(5):311-22
14760508
Mol Gen Genet. 1990 Sep;223(2):211-6
2250648
Nucleic Acids Res. 1991 Aug 11;19(15):4083-9
1651475
RNA. 2008 Sep;14(9):1704-13
18676618
Saline Syst. 2005 Jul 04;1:2
16176593