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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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Size distribution of ultrasmall introns in chlorarachniophyte nucleomorph genes. The total number of introns in each size category is indicated by color bars: B. natans (pink), A. amoebiformis (red), L. vacuolata (blue), and L. oceanica (green).
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evv096-F4: Size distribution of ultrasmall introns in chlorarachniophyte nucleomorph genes. The total number of introns in each size category is indicated by color bars: B. natans (pink), A. amoebiformis (red), L. vacuolata (blue), and L. oceanica (green).

Mentions: The chlorarachniophyte nucleomorph genomes are known to have numerous ultrasmall spliceosomal introns ranging from 18 to 23 nt (865 and 1,021 in B. natans and L. oceanica, respectively), whereas cryptophyte nucleomorphs have a small number of introns (0–24) (Lane et al. 2007; Moore et al. 2012). In this study, we predicted 793 and 1,028 of ultrasmall introns in A. amoebiformis and L. vacuolata, respectively (table 1). Most of these introns are 18–23 nt in size and possess a typical spliceosomal boundary (5′-GT and AG-3′), which is similar to that observed in other chlorarachniophytes (fig. 4). A remarkable difference of introns among four chlorarachniophyte nucleomorph genomes is the size distribution (fig. 4). The proportion of 19-nt introns is the highest in B. natans (70.3%) and L. oceanica (49.3%), whereas 18- and 20-nt introns are abundant in A. amoebiformis (42.1%) and L. vacuolata (35.8%), respectively. Total intron sizes are 14.9, 16.5, 20.0, and 20.9 kb in A. amoebiformis, B. natans, L. oceanica, and L. vacuolata, respectively. A positive correlation between the nucleomorph genome size and the intron length was assumed (Tanifuji et al. 2014), but our data do not support this hypothesis. Although most of the introns are 18–23 nt in size, we found two exceptional introns that were 40 and 41 nt in size in the different positions of A. amoebiformis and L. vacuolata prp43-2 genes, respectively (supplementary fig. S1, Supplementary Material online). These introns could be derived from the fusion of two ultrasmall introns because a relict AG boundary exists at the center of the introns. Lotharella oceanica prp43-2 also has a 32-nt intron (Tanifuji et al. 2014) at the same position as that of the 40-nt intron in A. amoebiformis, which would be the result of size reduction, following the intron fusion.Fig. 4.—


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

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

Size distribution of ultrasmall introns in chlorarachniophyte nucleomorph genes. The total number of introns in each size category is indicated by color bars: B. natans (pink), A. amoebiformis (red), L. vacuolata (blue), and L. oceanica (green).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv096-F4: Size distribution of ultrasmall introns in chlorarachniophyte nucleomorph genes. The total number of introns in each size category is indicated by color bars: B. natans (pink), A. amoebiformis (red), L. vacuolata (blue), and L. oceanica (green).
Mentions: The chlorarachniophyte nucleomorph genomes are known to have numerous ultrasmall spliceosomal introns ranging from 18 to 23 nt (865 and 1,021 in B. natans and L. oceanica, respectively), whereas cryptophyte nucleomorphs have a small number of introns (0–24) (Lane et al. 2007; Moore et al. 2012). In this study, we predicted 793 and 1,028 of ultrasmall introns in A. amoebiformis and L. vacuolata, respectively (table 1). Most of these introns are 18–23 nt in size and possess a typical spliceosomal boundary (5′-GT and AG-3′), which is similar to that observed in other chlorarachniophytes (fig. 4). A remarkable difference of introns among four chlorarachniophyte nucleomorph genomes is the size distribution (fig. 4). The proportion of 19-nt introns is the highest in B. natans (70.3%) and L. oceanica (49.3%), whereas 18- and 20-nt introns are abundant in A. amoebiformis (42.1%) and L. vacuolata (35.8%), respectively. Total intron sizes are 14.9, 16.5, 20.0, and 20.9 kb in A. amoebiformis, B. natans, L. oceanica, and L. vacuolata, respectively. A positive correlation between the nucleomorph genome size and the intron length was assumed (Tanifuji et al. 2014), but our data do not support this hypothesis. Although most of the introns are 18–23 nt in size, we found two exceptional introns that were 40 and 41 nt in size in the different positions of A. amoebiformis and L. vacuolata prp43-2 genes, respectively (supplementary fig. S1, Supplementary Material online). These introns could be derived from the fusion of two ultrasmall introns because a relict AG boundary exists at the center of the introns. Lotharella oceanica prp43-2 also has a 32-nt intron (Tanifuji et al. 2014) at the same position as that of the 40-nt intron in A. amoebiformis, which would be the result of size reduction, following the intron fusion.Fig. 4.—

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