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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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Comparison of gene content among nucleomorph genomes. (A) Comparison of gene content among four chlorarachniophyte nucleomorph genomes. Venn diagrams indicate the number of shared and/or unique genes categorized as total protein-coding genes, function-predicted protein genes, and hypothetical protein genes (ORFans). (B) Comparison of conserved core genes between four chlorarachniophytes and four cryptophytes. Total 93 function-predicted genes are overlapped among eight nucleomorph genomes of chlorarachniophytes and cryptophytes. Light Venn diagrams show the number of shared and/or unique genes in each functional category.
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evv096-F3: Comparison of gene content among nucleomorph genomes. (A) Comparison of gene content among four chlorarachniophyte nucleomorph genomes. Venn diagrams indicate the number of shared and/or unique genes categorized as total protein-coding genes, function-predicted protein genes, and hypothetical protein genes (ORFans). (B) Comparison of conserved core genes between four chlorarachniophytes and four cryptophytes. Total 93 function-predicted genes are overlapped among eight nucleomorph genomes of chlorarachniophytes and cryptophytes. Light Venn diagrams show the number of shared and/or unique genes in each functional category.

Mentions: The nucleomorph genomes of four chlorarachniophytes, A. amoebiformis, B. natans, L. vacuolata, and L. oceanica, share 189 protein-coding genes, including 171 function-predicted genes and 18 ORFans (fig. 3A and supplementary table S1, Supplementary Material online). Total 198 function-predicted genes have been annotated in chlorarachniophyte nucleomorph genomes, and 86% (171/198) of them are overlapped among four genomes (fig. 3A). In cryptophytes, 69% (216/311) function-predicted genes are shared among four nucleomorph genomes (Moore et al. 2012), suggesting that chlorarachniophyte nucleomorph genomes are less diverse than cryptophyte ones in term of gene content. Interestingly, all four chlorarachniophyte nucleomorphs possess the same set of genes encoding 17 plastid-associated proteins. The other annotated genes mainly encode housekeeping proteins for transcription, translation, DNA/RNA metabolism, and protein folding/degradation, and these genes would remain in the nucleomorph genomes for expression of the 17 plastid-associated proteins. When content of nucleomorph conserved core genes in four chlorarachniophytes was compared with those in four cryptophytes, 93 of 171 chlorarachniophyte core genes (54%) were overlapped with the cryptophyte core genes (fig. 3B). Shared genes in the both groups were found in multiple categories of eukaryotic housekeeping functions (e.g., translation, transcription, DNA/RNA metabolism, and protein fate and degradation), and half of shared genes (49/93 genes) were categorized as translation (fig. 3B). These data suggest that there are similar reductive pressures on nucleomorph-retained genes in both chlorarachniophytes and cryptophytes.Fig. 3.—


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

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

Comparison of gene content among nucleomorph genomes. (A) Comparison of gene content among four chlorarachniophyte nucleomorph genomes. Venn diagrams indicate the number of shared and/or unique genes categorized as total protein-coding genes, function-predicted protein genes, and hypothetical protein genes (ORFans). (B) Comparison of conserved core genes between four chlorarachniophytes and four cryptophytes. Total 93 function-predicted genes are overlapped among eight nucleomorph genomes of chlorarachniophytes and cryptophytes. Light Venn diagrams show the number of shared and/or unique genes in each functional category.
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Related In: Results  -  Collection

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evv096-F3: Comparison of gene content among nucleomorph genomes. (A) Comparison of gene content among four chlorarachniophyte nucleomorph genomes. Venn diagrams indicate the number of shared and/or unique genes categorized as total protein-coding genes, function-predicted protein genes, and hypothetical protein genes (ORFans). (B) Comparison of conserved core genes between four chlorarachniophytes and four cryptophytes. Total 93 function-predicted genes are overlapped among eight nucleomorph genomes of chlorarachniophytes and cryptophytes. Light Venn diagrams show the number of shared and/or unique genes in each functional category.
Mentions: The nucleomorph genomes of four chlorarachniophytes, A. amoebiformis, B. natans, L. vacuolata, and L. oceanica, share 189 protein-coding genes, including 171 function-predicted genes and 18 ORFans (fig. 3A and supplementary table S1, Supplementary Material online). Total 198 function-predicted genes have been annotated in chlorarachniophyte nucleomorph genomes, and 86% (171/198) of them are overlapped among four genomes (fig. 3A). In cryptophytes, 69% (216/311) function-predicted genes are shared among four nucleomorph genomes (Moore et al. 2012), suggesting that chlorarachniophyte nucleomorph genomes are less diverse than cryptophyte ones in term of gene content. Interestingly, all four chlorarachniophyte nucleomorphs possess the same set of genes encoding 17 plastid-associated proteins. The other annotated genes mainly encode housekeeping proteins for transcription, translation, DNA/RNA metabolism, and protein folding/degradation, and these genes would remain in the nucleomorph genomes for expression of the 17 plastid-associated proteins. When content of nucleomorph conserved core genes in four chlorarachniophytes was compared with those in four cryptophytes, 93 of 171 chlorarachniophyte core genes (54%) were overlapped with the cryptophyte core genes (fig. 3B). Shared genes in the both groups were found in multiple categories of eukaryotic housekeeping functions (e.g., translation, transcription, DNA/RNA metabolism, and protein fate and degradation), and half of shared genes (49/93 genes) were categorized as translation (fig. 3B). These data suggest that there are similar reductive pressures on nucleomorph-retained genes in both chlorarachniophytes and cryptophytes.Fig. 3.—

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