ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection

Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined) characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a perpeak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG), an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors

Μελέτες γενετικής πληθυσμών, γενετικής χαρτογράφησης και συγκριτικής γονιδιωματικής σε ελληνικά είδη ιχθύων με την χρήση πολυμορφισμών ...

In the current study, we focused on two marine fish species, the striped red mullet Mullus surmuletus and the gilthead sea bream Sparus aurata, fish with high socio-economic value. In the last part we examined the freshwater species, Valencia letourneuxi, whose conservation is of great importance due to extinction factors. Different populations across the distribution area of each species were collected and further processed. Our analyses were performed by combining two different types of molecular markers; microsatellite and mitochondrial loci. The aim of the study was the revelation of the phylogeographic relations among the populations of each species leading to the distribution patterns that may explain the evolutionary processes. The genetic structure as well as the genetic variation displayed, improved the comprehension of the diversity motifs present in the Atlantic-Mediterranean area. Possible explanations for these patterns are analyzed, suggesting gene flow and bottleneck phenomena along with environmental factors influencing the distribution localities. Palaeoclimatic and palaeogeographic events also played a crucial role in the formation of the population expansion and differentiation. This study offers opportunities in the future understanding of the phylogeography of marine populations figuring the role of genetic variation in functional, developmental and evolutionary basis.Η παρούσα μελέτη επικεντρώθηκε σε δύο θαλάσσια είδη, το Mullus surmuletus (κοινή ονομασία μπαρμπούνι) και το Sparus aurata (κοινή ονομασία τσιπούρα), ψάρια με μεγάλη κοινωνική-οικονομική αξία. Στο τελευταίο κεφάλαιο, εξετάστηκε ένα είδος εσωτερικών υδάτων, το Valencia letourneuxi (κοινή ονομασία ζουρνάς), του οποίου η διατήρηση είναι εξαιρετικά μεγάλης σημασίας καθώς το είδος βρίσκεται υπό εξαφάνιση. Διαφορετικοί πληθυσμοί κατά μήκος του εύρους κατανομής κάθε είδους συλλέχθησαν για περαιτέρω επεξεργασία. Οι αναλύσεις πραγματοποιήθηκαν κατόπιν συνδυασμού δυο διαφορετικών τύπων μοριακών δεικτών, του μικροδορυφορικού και μιτοχονδριακού DNA. Στόχος της μελέτης ήταν η αποκάλυψη των φυλογενετικών σχέσεων ανάμεσα στους πληθυσμούς κάθε είδους, με σκοπό την εύρεση των προτύπων κατανομής που εξηγούν τις εξελικτικές διαδικασίες. Η γενετική δομή, όπως και η γενετική ποικιλότητα που αναδείχθηκαν, βελτίωσαν την κατανόηση των μοτίβων ποικιλομορφίας, παρόντα στις περιοχές του Ατλαντικού Ωκεανού και της Μεσογείου Θάλασσας. Πιθανές εξηγήσεις για τα μοτίβα που παρατηρήθηκαν υποδηλώνουν γονιδιακή ροή και φαινόμενα στενωπού μαζί με περιβαλλοντικούς παράγοντες που επηρεάζουν τις τοποθεσίες κατανομής. Επιπλέον, παλαιοκλιματικά και παλαιογεωγραφικά γεγονότα έπαιξαν σημαντικό ρόλο στη διαμόρφωση της πληθυσμιακής εξάπλωσης και διαφοροποίησης. Συνεπώς, μελλοντικές ευκαιρίες για την κατανόηση της φυλογεωγραφίας θαλάσσιων πληθυσμών προσφέρονται, αποκαλύπτοντας το ρόλο της γενετικής ποικιλομορφίας σε λειτουργική, αναπτυξιακή και εξελικτική βάση

Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic

Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu

Saurata_Alleles_Dryad

Microsatellites' allele

Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.

International audienceAn updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L, a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 ESTSSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7 cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6 cM, with an average of 5.75 cM. The male and female maps have a length of 1349.2 and 2172.1 cM, respectively, and the average distance between markers is 4.38 and 7.05 cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome