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

Abstract

Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict nucleus, so-called the nucleomorph, of the green and red algal endosymbiont, respectively. Nucleomorph genomes are an interesting and suitable model to study the reductive evolution of endosymbiotically derived genomes. To date, nucleomorph genomes have been sequenced in four cryptophyte species and two chlorarachniophyte species, including Bigelowiella natans (373 kb) and Lotharella oceanica (610 kb). In this study, we report complete nucleomorph genome sequences of two chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata, to gain insight into the reductive evolution of nucleomorph genomes in the chlorarachniophytes. The nucleomorph genomes consist of three chromosomes totaling 374 and 432 kb in size in A. amoebiformis and L. vacuolata, respectively. 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. This suggests that chlorarachniophyte nucleomorph genomes underwent most of their reductive evolution prior to the radiation of extent members of the group. 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.

Keywords: chlorarachniophyte; endosymbiosis; genome reduction; nucleomorph; secondary plastid.

Fig. 1.—

Nucleomorph genome map of the chlorarachniophyte A. amoebiformis. The genome is comprised three chromosomes, which are shown as being 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. Syntenic regions with B. natans (blue), L. vacuolata (red), L. oceanica (gray), and both L. vacuolata and L. oceanica (green) are shaded by color gradations.

Fig. 2.—

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.

Fig. 3.—

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.

Fig. 4.—

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).

Fig. 5.—

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.

Fig. 6.—

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.