PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets

Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. 

Available datasets: 

- reference file for regions selected for amplicon sequencing: Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa

- final .bam files containing processed PacBio sequencing reads aligned to the reference:

PacBio_amplicon_seq_T1.bam  and PacBio_amplicon_seq_T6.bam 

- . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: 

P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table and P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table

Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%).  Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.