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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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Degraded ORFans in syntenic blocks of chlorarachniophyte nucleomorph genomes. Functions of annotated genes and ORFan genes are shown in gray and black boxes, respectively. Gray highlights indicate syntenic positions between different nucleomorph genomes. Red highlights show the correspondence of syntenic ORFans and functional annotated genes that occupy the same syntenic positions. (A) The mcm-like gene of B. natans corresponds to an ORFan of A. amoebiformis. (B) tcpG genes of three chlorarachniophytes occupy the same syntenic position as that of an ORFan in A. amoebiformis. (C) The L. oceanica tbl3 gene corresponds to an ORFan in L. vacuolata. (D) The L. vacuolata nop56 gene corresponds to two ORFans in L. oceanica.
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evv096-F6: Degraded ORFans in syntenic blocks of chlorarachniophyte nucleomorph genomes. Functions of annotated genes and ORFan genes are shown in gray and black boxes, respectively. Gray highlights indicate syntenic positions between different nucleomorph genomes. Red highlights show the correspondence of syntenic ORFans and functional annotated genes that occupy the same syntenic positions. (A) The mcm-like gene of B. natans corresponds to an ORFan of A. amoebiformis. (B) tcpG genes of three chlorarachniophytes occupy the same syntenic position as that of an ORFan in A. amoebiformis. (C) The L. oceanica tbl3 gene corresponds to an ORFan in L. vacuolata. (D) The L. vacuolata nop56 gene corresponds to two ORFans in L. oceanica.

Mentions: Nucleomorph syntenic blocks contain several ORFans, the so-called syntenic ORFans, encoding nucleomorph-specific hypothetical proteins. It is difficult to predict the origins and functions of ORFans because of their high sequence diversity. However, syntenic ORFans have the potential for estimating homologous genes through comparison of positions and coding gene sizes among different nucleomorph genomes. In cryptophytes, a portion of ORFans are located at the same syntenic position as functional annotated genes found in the other nucleomorph genomes, suggesting that those ORFans originated by diversification of the annotated genes (Lane et al. 2007; Moore et al. 2012). Our comparative analysis detected several syntenic ORFans in chlorarachniophyte nucleomorph genomes (fig. 6). The 594-amino acid coding ORFan (orf594) of A. amoebiformis is located between rad25 and eif6, and the mcm-like gene composed of 606 amino acids occupies the same syntenic position of B. natans (fig. 6A). Amorphochlora amoebiformis possesses the 486-amino acid ORFan (orf486) next to rpl2, whereas the other three chlorarachniophytes have tcpG genes (480–506 amino acids) at the same position (fig. 6B). The L. vacuolata orf776 between mce and U5 snRNP (116 kDa) is located in the same syntenic position of L. oceanica tbl3 (780 amino acids) (fig. 6C). These data suggest that nucleomorph-encoded ORFans are generated by sequence divarication of functional annotated protein genes in both chlorarachniophytes and cryptophytes. However, it remains unclear whether ORFans still have the original function of homologous genes or not.Fig. 6.—


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

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

Degraded ORFans in syntenic blocks of chlorarachniophyte nucleomorph genomes. Functions of annotated genes and ORFan genes are shown in gray and black boxes, respectively. Gray highlights indicate syntenic positions between different nucleomorph genomes. Red highlights show the correspondence of syntenic ORFans and functional annotated genes that occupy the same syntenic positions. (A) The mcm-like gene of B. natans corresponds to an ORFan of A. amoebiformis. (B) tcpG genes of three chlorarachniophytes occupy the same syntenic position as that of an ORFan in A. amoebiformis. (C) The L. oceanica tbl3 gene corresponds to an ORFan in L. vacuolata. (D) The L. vacuolata nop56 gene corresponds to two ORFans in L. oceanica.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494063&req=5

evv096-F6: Degraded ORFans in syntenic blocks of chlorarachniophyte nucleomorph genomes. Functions of annotated genes and ORFan genes are shown in gray and black boxes, respectively. Gray highlights indicate syntenic positions between different nucleomorph genomes. Red highlights show the correspondence of syntenic ORFans and functional annotated genes that occupy the same syntenic positions. (A) The mcm-like gene of B. natans corresponds to an ORFan of A. amoebiformis. (B) tcpG genes of three chlorarachniophytes occupy the same syntenic position as that of an ORFan in A. amoebiformis. (C) The L. oceanica tbl3 gene corresponds to an ORFan in L. vacuolata. (D) The L. vacuolata nop56 gene corresponds to two ORFans in L. oceanica.
Mentions: Nucleomorph syntenic blocks contain several ORFans, the so-called syntenic ORFans, encoding nucleomorph-specific hypothetical proteins. It is difficult to predict the origins and functions of ORFans because of their high sequence diversity. However, syntenic ORFans have the potential for estimating homologous genes through comparison of positions and coding gene sizes among different nucleomorph genomes. In cryptophytes, a portion of ORFans are located at the same syntenic position as functional annotated genes found in the other nucleomorph genomes, suggesting that those ORFans originated by diversification of the annotated genes (Lane et al. 2007; Moore et al. 2012). Our comparative analysis detected several syntenic ORFans in chlorarachniophyte nucleomorph genomes (fig. 6). The 594-amino acid coding ORFan (orf594) of A. amoebiformis is located between rad25 and eif6, and the mcm-like gene composed of 606 amino acids occupies the same syntenic position of B. natans (fig. 6A). Amorphochlora amoebiformis possesses the 486-amino acid ORFan (orf486) next to rpl2, whereas the other three chlorarachniophytes have tcpG genes (480–506 amino acids) at the same position (fig. 6B). The L. vacuolata orf776 between mce and U5 snRNP (116 kDa) is located in the same syntenic position of L. oceanica tbl3 (780 amino acids) (fig. 6C). These data suggest that nucleomorph-encoded ORFans are generated by sequence divarication of functional annotated protein genes in both chlorarachniophytes and cryptophytes. However, it remains unclear whether ORFans still have the original function of homologous genes or not.Fig. 6.—

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