Intra-genomic rDNA polymorphism in Radiolaria

In this study, we assess both (i) the intra-genomic variability within two groups of Radiolaria and (ii) whether long-read sequencing provides a reliable source of diversity estimation suitable for environmental molecular surveys. Briefly, our results highlight that intra-genomic variability is taxa dependent leading to over-estimation of the diversity in specific specimens. We show that short-read sequencing must be subjected to careful interpretation, especially of low abundant reads due to rDNA copy number biases among different organisms, cross-contamination or tag-jumping among other reasons. Lastly, we demonstrate that long-read sequencing produces an accurate and reliable phylogenetic signal despite high error rate, after bioinformatic processing. We therefore encourage future environmental molecular surveys to dedicate efforts on long-read sequencing, accessing not only uncultured environmental diversity richness but also its phylogenetic information.To demultiplex files:Sanger: The fasta file contains the sequences with the following sequence names: "Cell-identifier_primer_replicate_well"; please note the underscore delimiting fields.Illumina: The structure of the table below is as follows: "cell-identifier_replicate\tbarcode"; please note the tabulation ("\t") delimiting columns and different replicates in new columns ("\n").Mge17-9_M8R36\tCGCACCTT\nMge17-9_M8R38\tATACATGG\nMge17-9_M8R40\tAACAGACA\nVil496_M8R6\tAATGGAGG\nVil496_M8R7\tTTCTCCTG\nVil496_M8R8\tCTTCTTCA\nVil490_M8R19\tCGCAAGCA\nVil490_M8R20\tCCAGTCAG\nVil490_M8R23\tCTATAAGT\nMge17-124_M8R41\tTATCCAGG\nMge17-124_M8R25\tAACACCGT\nMge17-124_M8R26\tATGTATAA\nMge17-81_M8R9\tCGCAACAG\nMge17-81_M8R10\tAACAATGG\nMge17-81_M8R12\tGAGTACTA\nVil497_M8R28\tTATCAGGA\nVil497_M8R29\tGCGACAAT\nVil497_M8R30\tGTCGGTCA\nMge17-82_M8R15\tTATCACAT\nMge17-82_M8R16\tGTCGCTGT\nMge17-82_M8R17\tCCGAGATT\nVil480_M8R31\tAACGAGTG\nVil480_M8R32\tAACACGTA\nVil480_M8R35\tTGATCCTAMinION: The structure of the table below is as follows: "cell-identifier_replicate\tbarcode"; please note the tabulation ("\t") delimiting columns.Vil325_BC01\tAAGAAAGTTGTCGGTGTCTTTGTG\nVil325_BC02\tTCGATTCCGTTTGTAGTCGTCTGT\nVil325_BC03\tGAGTCTTGTGTCCCAGTTACCAGG\nVil496_BC14\tAACGAGTCTCTTGGGACCCATAGA\nVil496_BC05\tCTTGTCCAGGGTTTGTGTAACCTT\nVil496_BC15\tAGGTCTACCTCGCTAACACCACTG\nMge17-81_BC07\tGTGTTACCGTGGGAATGAATCCTT\nMge17-81_BC08\tTTCAGGGAACAAACCAAGTTACGT\nMge17-81_BC09\tAACTAGGCACAGCGAGTCTTGGTT\nMge17-82_BC16\tCGTCAACTGACAGTGGTTCGTACT\nMge17-82_BC11\tGTTTCATCTATCGGAGGGAATGGA\nMge17-82_BC12\tCAGGTAGAAAGAAGCAGAATCGGA