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Fig. 2 | Genome Biology

Fig. 2

From: Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Fig. 2

a Violin plots displaying the “per gene” coverage of the protein-coding genes annotated in the mussel genomes, normalized by the expected haploid mussel genome size, calculated based on the mapping of Illumina PE libraries, and obtained either from the mantle or gills tissue.  “0”, “1” and “2” indicate the number of alleles per individual. b Summary of the “per base” coverage of the Lola assembly (evaluated by the mapping of Illumina PE reads obtained from the mantle tissue). Two main peaks of coverage are clearly visible, corresponding to the hemizygous (41.5X) and homozygous (83X) peaks of coverage based on genome size estimates. The peak located at 0 indicates approximately 70 Mb of genome assembly which did not achieve any mapping based on Q ≥ 60. c Circus plot summarizing the presence-absence variation phenomenon on the nine longest genome scaffolds, plus the scaffold 02822, which contains a large fraction of dispensable genes. Italian and Galician mussel genomes are indicated with green and blue shades of color, respectively. Full and empty circles indicate present and absent genes, respectively. Scaffold names, reported in clockwise order, are: s00009, s029833, s00073, s00003, s00002, s00060, s00247, s00011, s00241 and s00029. d Detail of presence-absence variation in the genomic scaffold 02822; note that this scaffold contains a single core gene and a large (about 45 kb) block of dispensable genes, which are only found in four out of the analyzed genomes (including Lola, where the gene block is present in a single copy only). Gene IDs are, from left to right, as follows: MGAL10A041721, MGAL10A025495, MGAL10A021236, MGAL10A038341, MGAL10A006169, MGAL10A040493, MGAL10A046398, MGAL10A002899, MGAL10A052538, MGAL10A016640, MGAL10A080632, MGAL10A080632, MGAL10A050728, MGAL10A069289, MGAL10A086703, MGAL10A046961, MGAL10A008710, MGAL10A090544, MGAL10A069343, MGAL10A077743 and MGAL10A011823

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