Intron characterization and their potential as molecular markers for population studies in the scallopsAequipecten opercularisandMimachlamys varia

Abstract

Exon-primed intron-crossing PCR was used on the European commercial scallops Aequipecten opercularis and Mimachlamys varia to characterize introns of four nuclear genes and to identify DNA markers useful for population studies. The primers used yielded the expected product, except those for the lysozyme gene that failed to work in M. varia and amplified a fragment of a proteasome subunit gene (APSM) in A. opercularis. According to the sequences characterized, A. opercularis has at least four calmodulin genes, one of arginine kinase and two of beta-tubulin, and M. varia five, one and one, respectively. Length polymorphism or/and restriction fragment length polymorphism was detected at two loci of A. opercularis (arginine kinase and APSM) and four of M. varia (calmodulin and beta-tubulin), distinguishing in each case two or three alleles. The polymorphic loci were not closely linked. The population survey included four localities from Spain and one from Northern Ireland for A. opercularis and two Spanish localities for M. varia. Observed heterozygosity (H(o)) per locus was 0.276 and 0.296 in A. opercularis. The Northern Ireland sample had the lowest H(o) value (0.200) and the Mediterranean Spanish sample the highest (0.350). In M. varia, H(o) per locus ranged from 0.172 to 0.391 and the two localities showed similar H(o) values (0.255 and 0.293). All population-locus combinations were in agreement with Hardy-Weinberg equilibrium, except two loci of M. varia that showed a strong heterozygote deficit in the two localities examined. Evidence for genetic differentiation among samples was not found.

Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii) in China from Mitochondrial Control Region and Nuclear Intron Sequences

“…It is generally suitable for analyzing evolution, population genetic diversity and phylogenetic relationships among intraspecific populations. Furthermore, unlike exons, the intron sequences appear to be subject to little functional constraint and accumulates mutations rapidly, displaying high genetic variation [ 22 , 23 ]. Powerful analyses of population structure and related studies require information from multiple genetic loci [ 24 ].…”

The genome sequence of the variegated scallop, Mimachlamys varia (Linnaeus, 1758)

“…Various genetic studies of M. varia have been published ( Arias et al , 2009b ; Arias et al , 2009a ; Beajmont & Beveridge, 1984 ; Breitwieser et al , 2018 ; Fernandez-Moreno et al , 2008 ), most notably the sequencing of its transcriptome ( Viricel et al , 2018 ) and whole mitochondrial genome ( Malkócs et al , 2022 ). Here we present the chromosomally complete genome sequence for M. varia , sequenced as part of the Darwin Tree of Life Project.…”