Isolation and characterization of microsatellite markers for the red alga Porphyra umbilicalis

Abstract

The red algal genus Porphyra is sister to the genus Pyropia, the single most valuable marine crop in the Orient. We developed microsatellite loci for the red alga Porphyra umbilicalis, a widespread species in the Northern Atlantic. Enriched DNA libraries were constructed and 68 loci were screened for amplification and polymorphism. Seven polymorphic microsatellite markers were isolated using 44 individuals collected from four natural populations. The number of alleles per locus ranged from two to 12. Null alleles were detected in three loci. Among the markers reported, we tested also cross-amplification with two other Porphyra spp. These polymorphic microsatellite markers should be useful for investigating population genetic structure of P. umbilicalis in the North East Atlantic.

Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity

“…Genomic DNA was isolated from 238 P. linearis individuals and 152 P. dioica individuals using the LiCl extraction protocol described by Hong et al (1992) as modified by van Oppen et al (1995). Polymerase chain reaction (PCR) for 10 selected microsatellite markers (Varela-Álvarez et al, 2017(Varela-Álvarez et al, , 2018a; Supplementary Table 1) were performed separately for each locus in a 20 µl reaction volume containing 5-50 ng genomic DNA. Amplifications were conducted following the PCR programs and conditions as described in Varela-Álvarez et al (2017Varela-Álvarez et al ( , 2018a) using a GeneAmp 2720 thermal cycler (Applied Biosystems).…”

“…Polymerase chain reaction (PCR) for 10 selected microsatellite markers (Varela-Álvarez et al, 2017(Varela-Álvarez et al, , 2018a; Supplementary Table 1) were performed separately for each locus in a 20 µl reaction volume containing 5-50 ng genomic DNA. Amplifications were conducted following the PCR programs and conditions as described in Varela-Álvarez et al (2017Varela-Álvarez et al ( , 2018a) using a GeneAmp 2720 thermal cycler (Applied Biosystems). Amplified fragments were separated electrophoretically using an ABI PRISM 3130xl (Applied Biosystems) automated capillary sequencer at CCMAR, Portugal, and sized with GeneScan-350ROX size standard (Applied Biosystems).…”

“…Hybridization and introgression have also been reported for species from the Northeast Atlantic (Mols-Mortensen et al, 2012). The detection of introgression, mixoploidy, chimerism and cryptic diversity was impeded by the previous lack of molecular markers allowing sufficient resolution at both the individual and population level for European species of Porphyra; these have only recently become available (Varela-Álvarez et al, 2017(Varela-Álvarez et al, , 2018a, allowing high-resolution genotyping of large numbers of samples, for more progress in this direction.…”

Speciation in the Cladophorales species flock of ancient Lake Baikal

“…The high number of alleles per locus indicates that polyploidy occurs in this group. Although this could be attributed to duplicated loci across the genome, the occurrence of more than two alleles in different loci indicates that polyploidy is most likely, as observed in other studies (Andreakis et al 2009, Varela-Álvarez et al 2017a).…”

“…Discovering more than two alleles in most loci was an interesting result as it indicates polyploidy in these taxa. Although this could be the outcome of amplification of duplicated loci across the genome, the occurrence of multiple alleles in different loci indicates that polyploidy is most likely, as observed in other studies (Varela-Álvarez et al 2017a(Varela-Álvarez et al , 2017b. The occurrence of polyploidy in this group required adjustments on the population genetics methods and analyses.…”