Development of microsatellite markers by de novo transcriptome sequencing of flatfish Cyclopsetta fimbriata and Syacium papillosum (family: Paralichthyidae)

Flounder fish Cyclopsetta fimbriata and Syacium papillosum (Family: Paralichidae) inhabit the Gulf of Mexico (GoM) where there is a constant menace of oil spill events. Both can be sentinel species for pollutants associated with human activities, but the absence of markers has hampered their genetic studies. In this study we constructed two de novo transcriptomes of C. fimbriata and S. papillosum collected at 40–100 m below the sea surface and were used to develop microsatellite markers. A total of 42,273,686 and 38,304,544 raw reads were obtained for C. fimbriata and S. papillosum. After cleaning, we recovered 25,087,948 (59.3 %) reads with Q value >30 for S. papillosum and 22,062,086 (50 %) reads with Q value >30 for C. fimbriata. The transcriptome of C. fimbriata had 69,333 transcripts with an average GC content of 47.68 %. The length of contigs ranged from 248 bp to 15,452 bp, with an N50 length of 1608 bp. The S. papillosum transcriptome had 75,623 transcripts with an average GC content of 48.27 % with a length of contigs ranging from 181 bp to 16,638 bp, with an N50 length of 1582 bp. Then, 38 microsatellite loci for C. fimbriata and 40 microsatellite loci for S. papillosum were tested on 30 individuals of each species and 20 polymorphic microsatellite loci (50 %) were obtained for S. papillosum and 13 (34.21 %) for C. fimbriata. The Polymorphism Information Content (PIC) values were 0.8 for C. fimbriata and 0.9 for S. papillosum. Their utility for subsequent genetic population studies is discussed.