Background: The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related\nto adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to\nthe ability of this oyster to retain high concentrations of toxic heavy metals. There is, in addition, an unresolved\ncontroversy as to whether or not C. angulata and C. gigas are the same species or subspecies. Both oysters have 20\nmetacentric chromosomes of similar size that are morphologically indistinguishable. From a genomic perspective,\nas a result of the great variation and selection for heterozygotes in C. gigas, the assembly of its draft genome was\ndifficult: it is fragmented in more than seven thousand scaffolds.\nResults: In this work sixty BAC sequences of C. gigas downloaded from NCBI were assembled in BAC-contigs and\nassigned to BACs that were used as probes for mFISH in C. angulata and C. gigas. In addition, probes of H3, H4\nhistone, 18S and 5S rDNA genes were also used. Hence we obtained markers identifying 8 out the 10 chromosomes\nconstituting the karyotype. Chromosomes 1 and 9 can be distinguished morphologically. The bioinformatic analysis\ncarried out with the BAC-contigs annotated 88 genes. As a result, genes associated with abiotic adaptation, such as\nmetallothioneins, have been positioned in the genome. The gene ontology analysis has also shown many molecular\nfunctions related to metal ion binding, a phenomenon associated with detoxification processes that are characteristic\nin oysters. Hence the provisional integrated map obtained in this study is a useful complementary tool for the study of\noyster genomes.\nConclusions: In this study 8 out of 10 chromosome pairs of Crassostrea angulata/gigas were identified using BAC\nclones as probes. As a result all chromosomes can now be distinguished. Moreover, FISH showed that H3 and H4\nco-localized in two pairs of chromosomes different that those previously escribed. 88 genes were annotated in\nthe BAC-contigs most of them related with Molecular Functions of protein binding, related to the resistance of\nthe species to abiotic stress. An integrated genetic map anchored to the genome has been obtained in which\nthe BAC-contigs structure were not concordant with the gene structure of the C. gigas scaffolds displayed in the\nGenomicus database.
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