Microsatellite markers for the dinoflagellate Gambierdiscus caribaeus from high-throughput sequencing data

Abstract

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Development and characterisation of 16 novel microsatellite markers for the brown alga Sargassum fusiforme (Harvey) Setchell

“…The observed and expected heterozygosities ranged from 0.483 to 0.833 and 0.513 to 0.840 respectively. The number of alleles at each locus was similar to or higher than that at characterised microsatellite loci in other kelp species, such as Laminaria digitata (Liu et al, 2012), Gracilaria tenuistipitata (Song et al, 2014) and Gambierdiscus caribbaeus (Sassenhagen and Erdner, 2017).…”

First record of the spatial organization of the nucleosome‐less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

“…In G. australes, we found a nonrandom nuclear location of some microsatellites, including a high enrichment of poly C and especially the trinucleotide repeats ACC, ACG, ATC, AGG, and CCG; the presence of the latter defined the nuclear compartment referred to herein as the medulla. While microsatellites have frequently been used as molecular markers in dinoflagellates studies, including a study of Gambierdiscus (Sassenhagen and Erdner 2017), the chromosomal distributions of only four microsatellite motifs (AC, AG, GACA, and GATA) in three species of the genus Karenia have been reported. Those motifs were scattered over spherically shaped nuclei, with a particularly high density of AG repeats in one chromosome of Karenia selliformis and in one chromosome of Karenia mikimotoii (Cuadrado et al 2019).…”

Comparison of Spatial and Temporal Genetic Differentiation in a Harmful Dinoflagellate Species Emphasizes Impact of Local Processes

“…Seven microsatellites, four loci (G.carib1, G.carib2, G.carib3, and G.carib4) developed from shot-gun sequencing of the genome and three (G.caribT5, G.caribT6, and G.caribT7) discovered from a transcriptome (Sassenhagen and Erdner, 2017), were amplified in four separate PCR reactions. G.carib1, G.carib2, and G.caribT5 were amplified together in a 40 µl PCR reaction using an annealing temperature of 60 • C. G.caribT6 and G.caribT7 were amplified in duplex in 30 µl PCR reactions with an annealing temperature of 54 • C, and G.carib3 and G.carib4 were amplified individually in 15 µl PCR reactions (Sassenhagen and Erdner, 2017). The final PCR products were analyzed via capillary electrophoresis at the Genomics Core Lab, Texas A&M University, Corpus Christi.…”

“…When splitting the data set from the high-resolution sampling period at USVI into the three genetic clusters, pairwise linkage disequilibrium was detected in the early and middle cluster in one locus pair each respectively (USVI_1308-1403: G.carib1 and G.carib2, p = 0.009; USVI_1404-1510: G.carib1 and G.caribT7, p = 0.032). The previous F ST analysis (Table 3) highlighted the impact of two microsatellite markers that were discovered from a transcriptome (Sassenhagen and Erdner, 2017) for differentiation between USVI_1308-1403 and USVI_1404-1510. This observation was further emphasized by a STRUCTURE analysis restricted to the three transcriptomic microsatellites, which only detected two genetically distinct clusters: (1) the early sampling period (1308-1403) and (2) all remaining algal strains (1404-1604) ( Figure 4A).…”