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Fig. 3 | Genome Biology

Fig. 3

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

Fig. 3

a Validation of the presence-absence variation phenomenon by PCR, carried out on the genomic DNA extracted from the mantle (M) or gills (G) of the 14 mussel individuals subjected to whole-genome resequencing. In Lola, GALM6 and GALM11, genomic DNA was extracted from the mantle tissue only. One core gene (elongation factor 1 alpha) and two dispensable genes (E3 ubiquitin ligase 1 and myticalin B1) were tested. Tick and cross symbols indicate expectations based on the in silico analysis of whole-genome resequencing (WGR) data. b Observation of the presence-absence variation phenomenon by PCR carried out in 3 full-sib mussels obtained from a controlled cross (parents were also tested and are indicated by ♂ and ♀, respectively). One core gene (elongation factor 1 alpha) and two dispensable genes (E3 ubiquitin ligase 1 and myticalin B1) were tested. XEC19, XEC20, and XEC21 indicate the three mussel families subjected to this investigation. The original photographs of the agarose gels used for the preparation of this figure and technical details about these experiments are available in Additional file 1: Data Note 12. c Structure of the mussel pangenome, as exemplified by a Venn diagram representing the overlap between the gene sets found in Pura (a female individual previously sequenced by Murgarella and colleagues [18]) and in four resequenced genomes, i.e., ITAF1, ITAM1, GALF1, and GALM1 (note that all these genes are present in Lola). Genes shared by all individuals define the core genome, whereas genes shared by some, but not all, individuals are dispensable. The entire complement of core and dispensable genes defines the mussel pangenome. d Schematic overview of the possible origin of a gene presence-absence variation phenomenon. A cross between two parents carrying two core genes (A and C) and one dispensable gene (B) is depicted. In this case, both parents carry a single copy of the dispensable gene (i.e., the dispensable gene is present in a hemizygous genomic region). Based on Mendelian inheritance, PAV should be observed in 25% of the offspring produced by this cross. “0”, “1” and “2” indicate the expected number of copies of the dispensable gene

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