We just received the second set of data from the re-sequencing runs of our ENDEMIXIT samples. It is therefore time to write a short summary of what we got.
In total, more than five thousand of billions of DNA bases were sequenced, belonging to 121 individuals from 13 species: our five species of interest along with closely related species useful for comparative analyses. The sequencing product is a collection of reads, which are fragments of 150 bases of DNA (because of the sequencing machine technology, the genome has to be split into small units of DNA). On average, 313 million reads were produced for each of our individuals.
One critical parameter to assess the quality of a sequencing run is the coverage, which represents the number of times that a position in the genome is covered by a read. Our initial sequencing target was to reach a mean coverage of 15X for our diploid individuals (30X for the tetraploid sturgeon), and never accept a coverage lower that 2/3 of that. 90% of the individuals in the five focal species successfully exceeded this threshold, and we are very happy about the average coverage per species we obtained (see the Table below). Individuals not reaching the minimum targeted coverage will be re-analyzed or, in the worst case, substituted with other samples already collected.
Next steps: 1) concluding the sequencing of the individuals not analysed yet (six toads) and the 13 individuals that have not reached the minimum coverage; 2) ‘cleaning’ the reads (i.e. remove bad quality reads that can result from a bad reading from the sequencing machine) and align the reads to reference genomes in order to reconstruct the genomes of our individuals.
| Species | Number of individuals | Total amount data (billions of DNA bases) | Mean number of reads (million) | Mean coverage | Number of individuals with targeted coverage |
| The brown bear study (Marsican bear and Slovakian bear for comparison) | 22 | 905 | 274,2 | 17,9 | 21 |
| The Aeolian lizard study (Aolian lizard and Sicilian wall lizard for comparison) | 32 | 937 | 195,2 | 19,5 | 32 |
| The Ponza grayling study (Ponza grayling and other Hipparchia ssp. for comparison) | 22 | 198 | 60,0 | 18 | 22 |
| The Adriatic sturgeon study (Adriatic sturgeon and other Acipenser ssp. for comparison) | 30 | 1562 | 347,1 | 26 | 20 |
| The Apennine toad study (Apennine yellow-bellied toad, two populations from Northern and Southern Italy) | 15 | 2084 | 926,2 | 13,9 | 13 |
ENDEMIXIT 