De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics

Abstract

Patagonian toothfish (Dissostichus eleginoides) is a hefty notothenioid fish and a key species within the marine ecosystem with a high migratory capacity across sub-Antarctic and south American Pacific oceans. Transcriptome characterization and molecular markers associated with micro and macro-evolutionary studies are not available, which in turn limits the gain of knowledge about the genetic basis of this species. Therefore, in the present study, a de novo transcriptome from eight tissue and an embryonic state of Patagonian toothfish was developed, using the Illumina Hiseq 4000 platform. A total of 233,424 superTranscripts were assembled and 37,446 annotated against public databases. Moreover, we identified 71,107 expressed sequence tag-simple sequence repeats (EST-SSRs), with an average number of 0.3 SSRs per superTranscripts and one SSR per 1.12 kB. The most abundant SSR type was repeated dinucleotide (53.67%), followed by trinucleotide (13.73%) repeats. From the total of EST-SSRs identified, 34,196 primer pairs were properly designed and a subset of 25 immune loci were selected for its evaluation as potential EST-SSR population markers. Of this subset, 11 proved to have good technical features and were evaluated in 64 animals from four Patagonian toothfish populations. A number of 63 alleles were identified, with a mean of 4.9 alleles per locus and a polymorphism information content ranging from 0.224 to 0.591, with a mean of 0.50. Significant (F ST , range 0.082-0.117 and G ST , range 0.069-0.291) genetic differentiation (P < 0.05) was determined among the populations analyzed. Therefore, the results presented here represent a relevant genetic resource for biological studies on evolution, conservation, genetic diversity, population structure, and genetic management of breeding stocks of this important species.

Transcriptional Analyses of Acute Exposure to Methylmercury on Erythrocytes of Loggerhead Sea Turtle

“…These results support the high quality and integrity of our composite loggerhead transcriptome. Furthermore, these results are in agreement with those published in previous studies [ 59 , 60 , 61 ].…”

Comparative transcriptomics of spotted seatrout (Cynoscion nebulosus) populations to cold and heat stress

“…The N50 for our liver transcriptome was 3,121 base pairs (bp), much longer than similar de novo‐assembled transcriptomes for other fishes, including Yellow perch Perca falvescens (1,066 bp; Li et al, 2017), Spotted rainbowfish Melanotaenia duboulayi (1,856 bp; Smith et al., 2013), and Patagonian toothfish Dissostichus eleginoides (1,434 bp; Touma et al, 2019). The percentage of the BUSCO gene content present in the assembled transcriptome (87.4%) was higher than the gene content recovered for the European sardine Sardina pilchardus (82.1%; Machado et al, 2018), Patagonian toothfish Dissostichus eleginoides (78.92%; Touma et al, 2019), and Clown anemonefish Amphiprion percula (85.4%; Maytin et al, 2018). The high‐quality transcriptome can be attributed to the use of high‐quality samples, a combination of assemblers, and a range of k‐mers, as well as the subsequent redundancy‐reducing step.…”

SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis

“…Microsatellites or simple sequence repeats (SSRs) are tandem repeats of one to six nucleotides present in all eukaryotic genomes. Due to the high mutation rates, co-dominant inheritance, high abundance, reproducibility of microsatellite-based assays, extensive genome coverage, chromosome specific location, amenability to automation and high throughput genotyping ( Parida et al, 2009 ), SSRs have emerged as one of the most popular genetic markers in a wide range of applications in population genetics ( Filippi et al, 2015 ; Touma et al, 2019 ), conservation biology ( Han & An, 2009 ; Kalia et al, 2011 ; Longwu et al, 2012 ), marker-assisted selection (MAS) ( Parida et al, 2009 ; Che et al, 2014 ; Lv et al, 2014 ) and other studies ( Moore et al, 1999 ; Palmer et al, 2013 ; Parida et al, 2009 ). In addition, there is increasing evidence that SSRs can serve a functional role in the regulation of gene expression by affecting transcription, translational activity, DNA structure, and other metabolic activities ( Palmer et al, 2013 ).…”

“…With the wide application of high-throughput sequencing (HTS) technologies, especially for transcriptome sequencing, the development of SSR markers using HTS-based approaches has become a feasible alternative for many species ( Touma et al, 2019 ). This method has dramatically reduced the time and cost requirement for large-scale development of SSR markers compared to traditional methods ( Wu et al, 2014 ).…”