The lichen symbiosis re

The mycobiont is a single-spore isolate from C. grayi and the photobiont is Asterochloris glomerata isolated from C. grayi soredia [64]. Table 1 includes basic features of the two nuclear and the three organelle genomes. Organelle genomes are briefly discussed in Additional file 1, and details are in Xavier et al. [65] and Xavier’s thesis [66]. Whole genome assemblies and annotations are at [67] for the mycobiont and at [68] for the photobiont. Relationships of C. grayi and A.glomerata within broad phylogenetic contexts, genome sizes, and proportions of repeated and unique sequences are shown in Fig. 2. The nuclear genomes of lichen symbionts are not reduced in size nor gene content compared to free-living relatives, in contrast to the reductions observed in many host-dependent bacteria [69]. With its 35 Mb genome and 11,400 gene models, the C. grayi mycobiont falls in the average size range for most Ascomycota [70]. Other lichen fungi fall in the same range, between 26 and 59 Mb [46]. Large increases in the number of transposable elements significantly affect genome size in many biotrophic fungi [71], including the ectomycorrhizal ascomycetes T. melanosporum [58], E. granulatus [72], and C. geophilum [73] but this was not observed in C. grayi (Fig. 2). Like other Chlorophyta, A. glomerata has more and larger introns than fungi. Its genome (56 Mb and 10,000 gene models) is significantly smaller than that of C. reinhardtii (120 Mb) [49] but is larger than that of other Trebouxiophyceae like C. subellipsoideae C-169 (49 Mb) [54] and C. variabilis NC64A (46.2 Mb) [50] (Fig. 2). C. subellipsoideae C-169 is free-living, but the genus includes lichenized species [56, 74]. Chlorella NC64A is a facultative symbiont of ciliates and is host to large dsDNA viruses. Our analyses suggest that A. glomerata has also been host to large DNA viruses (A low-GC region in Asterochloris is a remnant of a large virus insertion, an HGT-mediator section), although a live virus has not yet been isolated from it. Over evolutionary time, chromosomal rearrangements left little synteny among the genomes of A. glomerata, Coccomyxa C-169 and Chlorella NC64A (Additional file 2).

Phylogenies, genome sizes and sequence distribution. Left side: Fungal (top) and algal (bottom) PhyML trees (LG + G + F + I) for C. grayi and A. glomerata involving, respectively, a random sample of 6000 and 4000 ungapped sites extracted from a concatenated alignment of 2137 and 683 orthologous protein families containing 794,828 and 159,356 ungapped sites. Bootstrap support values label internodes. Scales indicate nucleotide substitutions per site. Right side: Bars are proportional to genome size, and different shadings indicate the proportions of recent and older sequence replicas or of unique sequences. Duplicated sequences in genomes were revealed by BLAST alignment of the genomic sequence against itself at the nucleotide (BLASTN) or amino acid (TBLASTX) levels. The duplicated regions include regular genes as well as repeated elements (not yet fully characterized), but microsatellites and low complexity sequences were filtered out. Sequences that matched in both BLASTN and TBLASTX searches were only counted in the BLASTN category. Only alignments with e-values