Novel microsatellite markers suggest significant genetic isolation in the Eastern Pacific sponge Aplysina gerardogreeni.

BACKGROUND: The Eastern Tropical Pacific (ETP) harbors a great diversity of Porifera. In particular, the Aplysina genus has acquired biotechnological and pharmacological importance. Nevertheless, the ecological aspects of their species and populations have been poorly studied. Aplysina gerardogreeni is the most conspicuous verongid sponge from the ETP, where it is usually found on rocky-coralline ecosystems. We evaluated the polymorphism levels of 18 microsatellites obtained from next-generation sequencing technologies. Furthermore, we tested the null hypothesis of panmixia in A. gerardogreeni population from two Mexican-Pacific localities. METHODS AND RESULTS: A total of 6,128,000 paired reads were processed of which primer sets of 18 microsatellites were designed. The loci were tested in 64 specimens from Mazatlan, Sinaloa (N = 32) and Isabel Island, Nayarit (N = 32). The microsatellites developed were moderately polymorphic with a range of alleles between 2 and 11, and Ho between 0.069 and 0.785. Fifteen loci displayed significant deviation from the Hardy-Weinberg equilibrium. No linkage disequilibrium was detected. A strong genetic structure was confirmed between localities using hierarchical Bayesian analyses, principal coordinates analyses, and fixation indices (FST = 0.108*). All the samples were assigned to their locality; however, there was a small sign of mixing between localities. CONCLUSIONS: Despite the moderate values of diversity in microsatellites, they showed a strong signal of genetic structure between populations. We suggest that these molecular markers can be a relevant tool to evaluate all populations across the ETP. In addition, 17 of these microsatellites were successfully amplified in the species A. fistularis and A. lacunosa, meaning they could also be applied in congeneric sponges from the Caribbean Sea. The use of these molecular markers in population genetic studies will allow assessment of the connectivity patterns in species of the Aplysina genus.

Novel gene arrangement in the mitochondrial genome of the Cortés Geoduck clam (Panopea globosa).

The mitogenome of the Cortés geoduck clam Panopea globosa (Genbank accession KM580068) has a length of 15,469 bp and contains 13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNA genes, as conventional metazoan mitochondrial genomes. Structural genes start with ATG, ATA and GTG codons; whereas TAG and TAA are used as stop codons. Base composition is: 23.3% A, 40.4% T, 10.1% C and 26.1% G. As is typical of marine bivalves, all genes are coded on the same strand. On the other hand, the gene arrangement is considerably different from those found in other heterodont bivalve mitogenomes.

The complete mitochondrial DNA of the Pacific Geoduck clam (Panopea generosa).

The complete mitochondrial genome of the Pacific Geoduck Panopea generosa (Genbank accession KM580067) is 15,585 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA) found in metazoan mitogenomes, including the rare ATPase subunit 8 gene (ATP8). All genes are coded in the same strand but the gene arrangement is novel among heterodont bivalves. The base composition was: A 25.0%, T 38.7%, C 11.2% and G 25.0%. The genome is structurally similar to that of its congener the Cortes Geoduck Panopea globosa.

Complete mitochondrial genome of the beaubrummel Damselfish, Stegastes flavilatus (Pisces: Perciformes, Pomacentridae).

The mitogenome of the beaubrummel damselfish, Stegastes flavilatus Gill, 1862 (Genebank accession number KP136922), has a total length of 16,816 bp. It encodes 13 protein-coding, two ribosomal RNAs (rRNAs), and 22 transfer RNA (tRNA) genes. Base composition is 28.6% A, 26.0% T, 29.8% C, and 15.7% G and 45.5% GC content. The gene arrangement was found to be the same of other pomacentrid mitogenomes.