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Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata.

Suzuki S, Shirato S, Hirakawa Y, Ishida K - Genome Biol Evol (2015)

Bottom Line: Nucleomorph genomes are an interesting and suitable model to study the reductive evolution of endosymbiotically derived genomes.Comparative analyses among four chlorarachniophyte nucleomorph genomes revealed that these sequences share 171 function-predicted genes (86% of total 198 function-predicted nucleomorph genes), including the same set of genes encoding 17 plastid-associated proteins, and no evidence of a recent nucleomorph-to-nucleus gene transfer was found.However, there are slight variations in genome size, GC content, duplicated gene number, and subtelomeric regions among the four nucleomorph genomes, suggesting that the genomes might be undergoing changes that do not affect the core functions in each species.

View Article: PubMed Central - PubMed

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

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Nucleomorph genome map of the chlorarachniophyte L. vacuolata. The genome is comprised three chromosomes, which are shown artificially broken at their midpoint. Genes indicated on the right side are transcribed from top to bottom, and the genes on the left side are transcribed in the opposite direction. Colors of gene blocks correspond to predicted functional categories in the box. Duplicated gene regions (green) and syntenic regions with B. natans (blue), A. amoebiformis (red), L. oceanica (gray), and both B. natans and A. amoebiformis (yellow) are shaded by color gradations.
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evv096-F2: Nucleomorph genome map of the chlorarachniophyte L. vacuolata. The genome is comprised three chromosomes, which are shown artificially broken at their midpoint. Genes indicated on the right side are transcribed from top to bottom, and the genes on the left side are transcribed in the opposite direction. Colors of gene blocks correspond to predicted functional categories in the box. Duplicated gene regions (green) and syntenic regions with B. natans (blue), A. amoebiformis (red), L. oceanica (gray), and both B. natans and A. amoebiformis (yellow) are shaded by color gradations.

Mentions: The general characteristics of nucleomorph genomes in A. amoebiformis and L. vacuolata are summarized in table 1. Both nucleomorph genomes are composed of three chromosomes totaling 374.0 kb (131.9, 124.0, and 118.0 kb) in A. amoebiformis and 431.9 kb (166.2, 141.6, and 124.1 kb) in L. vacuolata. The actual genome sizes were slightly different from the predicted sizes, according to the PFGE analyses, approximately 330 and approximately 450 kb (Silver et al. 2007). The GC content is 30.0% and 24.7% in A. amoebiformis and L. vacuolata, respectively. The number of total genes is predicted to be 340, including 300 protein-coding genes, 21 tRNAs, 18 rRNAs, and 3 noncoding RNAs (ncRNAs) in the A. amoebiformis nucleomorph genome, and 359 genes, including 319 protein-coding genes, 19 tRNAs, 18 rRNAs, and 3 ncRNAs, in L. vacuolata (table 1). The gene density is 0.91 and 0.83 genes/kb in each nucleomorph genome (table 1). All three chromosomes of A. amoebiformis and L. vacuolata carry identical sequences in the six subtelomeric regions comprised an rDNA operon (SSU rDNA, 5.8S rDNA, and LSU rDNA) and the dnaK gene (figs. 1 and 2). When these genomes were compared with the nucleomorph genomes of two other chlorarachniophytes, B. natans and L. oceanica, all four nucleomorph genomes generally showed similar architectures; however, several notable variations were found.Fig. 1.—


Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata.

Suzuki S, Shirato S, Hirakawa Y, Ishida K - Genome Biol Evol (2015)

Nucleomorph genome map of the chlorarachniophyte L. vacuolata. The genome is comprised three chromosomes, which are shown artificially broken at their midpoint. Genes indicated on the right side are transcribed from top to bottom, and the genes on the left side are transcribed in the opposite direction. Colors of gene blocks correspond to predicted functional categories in the box. Duplicated gene regions (green) and syntenic regions with B. natans (blue), A. amoebiformis (red), L. oceanica (gray), and both B. natans and A. amoebiformis (yellow) are shaded by color gradations.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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evv096-F2: Nucleomorph genome map of the chlorarachniophyte L. vacuolata. The genome is comprised three chromosomes, which are shown artificially broken at their midpoint. Genes indicated on the right side are transcribed from top to bottom, and the genes on the left side are transcribed in the opposite direction. Colors of gene blocks correspond to predicted functional categories in the box. Duplicated gene regions (green) and syntenic regions with B. natans (blue), A. amoebiformis (red), L. oceanica (gray), and both B. natans and A. amoebiformis (yellow) are shaded by color gradations.
Mentions: The general characteristics of nucleomorph genomes in A. amoebiformis and L. vacuolata are summarized in table 1. Both nucleomorph genomes are composed of three chromosomes totaling 374.0 kb (131.9, 124.0, and 118.0 kb) in A. amoebiformis and 431.9 kb (166.2, 141.6, and 124.1 kb) in L. vacuolata. The actual genome sizes were slightly different from the predicted sizes, according to the PFGE analyses, approximately 330 and approximately 450 kb (Silver et al. 2007). The GC content is 30.0% and 24.7% in A. amoebiformis and L. vacuolata, respectively. The number of total genes is predicted to be 340, including 300 protein-coding genes, 21 tRNAs, 18 rRNAs, and 3 noncoding RNAs (ncRNAs) in the A. amoebiformis nucleomorph genome, and 359 genes, including 319 protein-coding genes, 19 tRNAs, 18 rRNAs, and 3 ncRNAs, in L. vacuolata (table 1). The gene density is 0.91 and 0.83 genes/kb in each nucleomorph genome (table 1). All three chromosomes of A. amoebiformis and L. vacuolata carry identical sequences in the six subtelomeric regions comprised an rDNA operon (SSU rDNA, 5.8S rDNA, and LSU rDNA) and the dnaK gene (figs. 1 and 2). When these genomes were compared with the nucleomorph genomes of two other chlorarachniophytes, B. natans and L. oceanica, all four nucleomorph genomes generally showed similar architectures; however, several notable variations were found.Fig. 1.—

Bottom Line: Nucleomorph genomes are an interesting and suitable model to study the reductive evolution of endosymbiotically derived genomes.Comparative analyses among four chlorarachniophyte nucleomorph genomes revealed that these sequences share 171 function-predicted genes (86% of total 198 function-predicted nucleomorph genes), including the same set of genes encoding 17 plastid-associated proteins, and no evidence of a recent nucleomorph-to-nucleus gene transfer was found.However, there are slight variations in genome size, GC content, duplicated gene number, and subtelomeric regions among the four nucleomorph genomes, suggesting that the genomes might be undergoing changes that do not affect the core functions in each species.

View Article: PubMed Central - PubMed

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

Show MeSH