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Polyploidy of endosymbiotically derived genomes in complex algae.

Hirakawa Y, Ishida K - Genome Biol Evol (2014)

Bottom Line: It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution.In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes.This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.

ABSTRACT
Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary endosymbiosis. The plastid is surrounded by four membranes, and a relict nucleus, called the nucleomorph, remains in the periplastidal compartment that is the remnant cytoplasm of the endosymbiont. Thus, these two algae possess four different genomes in a cell: Nuclear, nucleomorph, plastid, and mitochondrial. Recently, sequencing of the nuclear genomes of the chlorarachniophyte Bigelowiella natans and the cryptophyte Guillardia theta has been completed, and all four genomes have been made available. However, the copy number of each genome has never been investigated. It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution. In this study, we calculated genomic copy numbers in B. natans and G. theta using a real-time quantitative polymerase chain reaction approach. The nuclear genomes were haploid in both species, whereas the nucleomorph genomes were estimated to be diploid and tetraploid, respectively. Mitochondria and plastids contained a large copy number of genomic DNA in each cell. In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes. This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.

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Copy numbers of the four genomes in the chlorarachniophyte, Bigelowiella natans, and the cryptophyte, Guillardia theta. (A, B) Each bar shows the relative copy numbers of genomes (N, nuclear; Nm, nucleomorph; M, mitochondrial; P, plastid) calculated by real-time quantitative PCR in three independent experiments (samples A–C). The average value of the nuclear genome was set to 1.0, and other values were normalized. Error bars represent the standard deviation (SD) (n = 3–4). (C, D) Size and copy number of each genome are summarized in the cellular schemes.
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evu071-F1: Copy numbers of the four genomes in the chlorarachniophyte, Bigelowiella natans, and the cryptophyte, Guillardia theta. (A, B) Each bar shows the relative copy numbers of genomes (N, nuclear; Nm, nucleomorph; M, mitochondrial; P, plastid) calculated by real-time quantitative PCR in three independent experiments (samples A–C). The average value of the nuclear genome was set to 1.0, and other values were normalized. Error bars represent the standard deviation (SD) (n = 3–4). (C, D) Size and copy number of each genome are summarized in the cellular schemes.

Mentions: The copy numbers of nucleomorph chromosomes in B. natans and G. theta were predicted to be double to triple and quadruple that of nuclear chromosomes, respectively (fig. 1A and B). A stable copy number of nucleomorph chromosomes in G. theta was seen in three different DNA samples (fig. 1B), whereas the nucleomorph chromosome copy number of B. natans varied (fig. 1A). This variability was due to contamination by cells with divided plastids and nucleomorphs in the cultures; double plastids were detected by confocal laser microscopy in approximately 50% of cells (39 out of 75 cells) in sample C that showed a triple copy number of nucleomorph chromosomes (fig. 1A, supplementary fig. S1, Supplementary Material online). This suggests that the chromosome copy number of a single nucleomorph in B. natans is double that of nucleus. Three nucleomorph chromosomes indicated the same copy number in both species (fig. 1A and B), as previously seen by Southern blot analyses of pulsed-field gel separation that showed identical signal intensities of the three nucleomorph chromosomes (McFadden et al. 1994; Lane and Archibald 2006). Copy numbers of the B. natans mitochondrial and plastid genomes were approximately 18–40 and 30–50 times greater than that of the nuclear genome, respectively (fig. 1A). For G. theta, the mitochondrion and plastid contained approximately 24- to 43-fold and 130- to 260-fold more genomic copies than the nucleus, respectively (fig. 1B).Fig. 1.—


Polyploidy of endosymbiotically derived genomes in complex algae.

Hirakawa Y, Ishida K - Genome Biol Evol (2014)

Copy numbers of the four genomes in the chlorarachniophyte, Bigelowiella natans, and the cryptophyte, Guillardia theta. (A, B) Each bar shows the relative copy numbers of genomes (N, nuclear; Nm, nucleomorph; M, mitochondrial; P, plastid) calculated by real-time quantitative PCR in three independent experiments (samples A–C). The average value of the nuclear genome was set to 1.0, and other values were normalized. Error bars represent the standard deviation (SD) (n = 3–4). (C, D) Size and copy number of each genome are summarized in the cellular schemes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4007541&req=5

evu071-F1: Copy numbers of the four genomes in the chlorarachniophyte, Bigelowiella natans, and the cryptophyte, Guillardia theta. (A, B) Each bar shows the relative copy numbers of genomes (N, nuclear; Nm, nucleomorph; M, mitochondrial; P, plastid) calculated by real-time quantitative PCR in three independent experiments (samples A–C). The average value of the nuclear genome was set to 1.0, and other values were normalized. Error bars represent the standard deviation (SD) (n = 3–4). (C, D) Size and copy number of each genome are summarized in the cellular schemes.
Mentions: The copy numbers of nucleomorph chromosomes in B. natans and G. theta were predicted to be double to triple and quadruple that of nuclear chromosomes, respectively (fig. 1A and B). A stable copy number of nucleomorph chromosomes in G. theta was seen in three different DNA samples (fig. 1B), whereas the nucleomorph chromosome copy number of B. natans varied (fig. 1A). This variability was due to contamination by cells with divided plastids and nucleomorphs in the cultures; double plastids were detected by confocal laser microscopy in approximately 50% of cells (39 out of 75 cells) in sample C that showed a triple copy number of nucleomorph chromosomes (fig. 1A, supplementary fig. S1, Supplementary Material online). This suggests that the chromosome copy number of a single nucleomorph in B. natans is double that of nucleus. Three nucleomorph chromosomes indicated the same copy number in both species (fig. 1A and B), as previously seen by Southern blot analyses of pulsed-field gel separation that showed identical signal intensities of the three nucleomorph chromosomes (McFadden et al. 1994; Lane and Archibald 2006). Copy numbers of the B. natans mitochondrial and plastid genomes were approximately 18–40 and 30–50 times greater than that of the nuclear genome, respectively (fig. 1A). For G. theta, the mitochondrion and plastid contained approximately 24- to 43-fold and 130- to 260-fold more genomic copies than the nucleus, respectively (fig. 1B).Fig. 1.—

Bottom Line: It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution.In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes.This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.

ABSTRACT
Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary endosymbiosis. The plastid is surrounded by four membranes, and a relict nucleus, called the nucleomorph, remains in the periplastidal compartment that is the remnant cytoplasm of the endosymbiont. Thus, these two algae possess four different genomes in a cell: Nuclear, nucleomorph, plastid, and mitochondrial. Recently, sequencing of the nuclear genomes of the chlorarachniophyte Bigelowiella natans and the cryptophyte Guillardia theta has been completed, and all four genomes have been made available. However, the copy number of each genome has never been investigated. It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution. In this study, we calculated genomic copy numbers in B. natans and G. theta using a real-time quantitative polymerase chain reaction approach. The nuclear genomes were haploid in both species, whereas the nucleomorph genomes were estimated to be diploid and tetraploid, respectively. Mitochondria and plastids contained a large copy number of genomic DNA in each cell. In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes. This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.

Show MeSH