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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 homologous gene positions on nucleomorph genomes in four chlorarachniophytes. Colored blocks show three chromosomes in each nucleomorph genome: B. natans (green), A. amoebiformis (yellow), L. vacuolata (red), and L. oceanica (blue). The internal lines indicate paired homologous genes. Subtelomeric regions comprised an rDNA operon are excluded from this comparative analysis.
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evv096-F5: Comparison of homologous gene positions on nucleomorph genomes in four chlorarachniophytes. Colored blocks show three chromosomes in each nucleomorph genome: B. natans (green), A. amoebiformis (yellow), L. vacuolata (red), and L. oceanica (blue). The internal lines indicate paired homologous genes. Subtelomeric regions comprised an rDNA operon are excluded from this comparative analysis.

Mentions: Comparative analyses of nucleomorph genomes have revealed the existence of gene order conservation, so-called synteny, among distantly related species (Moore et al. 2012; Tanifuji et al. 2014). Lane et al. (2007) suggested that nonhomologous recombination events are likely to disrupt coding sequences in extremely reduced and compacted nucleomorph genomes. Therefore, recombination frequency is decreased, resulting in the retention of many syntenic blocks in nucleomorph genomes. In cryptophyte nucleomorphs, the average number of genes within a syntenic block consisting of four or more homologous genes, excluding ORFans, between two of G. theta, H. andersenii, Cr. paramecium, and Ch. mesostigmatica, is 6.7–19.4 (Moore et al. 2012). Our comparative analysis of four chlorarachniophyte nucleomorphs indicated that syntenic blocks were composed of 6.2 (n = 17), 5.9 (n = 13), and 5.8 (n = 14) genes between B. natans and A. amoebiformis, L. vacuolata, and L. oceanica, 6.5 (n = 11) genes between A. amoebiformis and L. vacuolata, 6.9 (n = 11) genes between A. amoebiformis and L. oceanica, and 11.5 (n = 21) genes between L. vacuolata and L oceanica, on average when the same definition as that used by Moore et al. (2012) was applied (fig. 5 and supplementary fig. S2, Supplementary Material online, and table 3). Nucleomorph genomes appear to be more scrambled in chlorarachniophytes than in cryptophytes. Even when two closely related Lotharella species (nucleus- and nucleomorph-encoded small subunit rDNAs are 95% and 99% identical, respectively, between L. vacuolata and L. oceanica) were compared, approximately 20% of the total genes (61/319 genes) were excluded from syntenic blocks in the L. vacuolata nucleomorph genome. Many of the syntenic blocks between L. vacuolata and L. oceanica are disrupted by duplicated gene regions (fig. 2). These data suggest that genomic rearrangement of chlorarachniophyte nucleomorphs seems to be under progression at the species level, and recombination frequency would be higher in duplicated regions.Fig. 5.—


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 homologous gene positions on nucleomorph genomes in four chlorarachniophytes. Colored blocks show three chromosomes in each nucleomorph genome: B. natans (green), A. amoebiformis (yellow), L. vacuolata (red), and L. oceanica (blue). The internal lines indicate paired homologous genes. Subtelomeric regions comprised an rDNA operon are excluded from this comparative analysis.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494063&req=5

evv096-F5: Comparison of homologous gene positions on nucleomorph genomes in four chlorarachniophytes. Colored blocks show three chromosomes in each nucleomorph genome: B. natans (green), A. amoebiformis (yellow), L. vacuolata (red), and L. oceanica (blue). The internal lines indicate paired homologous genes. Subtelomeric regions comprised an rDNA operon are excluded from this comparative analysis.
Mentions: Comparative analyses of nucleomorph genomes have revealed the existence of gene order conservation, so-called synteny, among distantly related species (Moore et al. 2012; Tanifuji et al. 2014). Lane et al. (2007) suggested that nonhomologous recombination events are likely to disrupt coding sequences in extremely reduced and compacted nucleomorph genomes. Therefore, recombination frequency is decreased, resulting in the retention of many syntenic blocks in nucleomorph genomes. In cryptophyte nucleomorphs, the average number of genes within a syntenic block consisting of four or more homologous genes, excluding ORFans, between two of G. theta, H. andersenii, Cr. paramecium, and Ch. mesostigmatica, is 6.7–19.4 (Moore et al. 2012). Our comparative analysis of four chlorarachniophyte nucleomorphs indicated that syntenic blocks were composed of 6.2 (n = 17), 5.9 (n = 13), and 5.8 (n = 14) genes between B. natans and A. amoebiformis, L. vacuolata, and L. oceanica, 6.5 (n = 11) genes between A. amoebiformis and L. vacuolata, 6.9 (n = 11) genes between A. amoebiformis and L. oceanica, and 11.5 (n = 21) genes between L. vacuolata and L oceanica, on average when the same definition as that used by Moore et al. (2012) was applied (fig. 5 and supplementary fig. S2, Supplementary Material online, and table 3). Nucleomorph genomes appear to be more scrambled in chlorarachniophytes than in cryptophytes. Even when two closely related Lotharella species (nucleus- and nucleomorph-encoded small subunit rDNAs are 95% and 99% identical, respectively, between L. vacuolata and L. oceanica) were compared, approximately 20% of the total genes (61/319 genes) were excluded from syntenic blocks in the L. vacuolata nucleomorph genome. Many of the syntenic blocks between L. vacuolata and L. oceanica are disrupted by duplicated gene regions (fig. 2). These data suggest that genomic rearrangement of chlorarachniophyte nucleomorphs seems to be under progression at the species level, and recombination frequency would be higher in duplicated regions.Fig. 5.—

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