DOI: 10.5061/dryad.31733
title: Data from: Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

description: Next generation sequencing allows access to a large quantity of genomic
 data. In plants, several studies used whole chloroplast genome sequences
 for inferring phylogeography or phylogeny. Even though the chloroplast is
 a haploid organelle, NGS plastome data identified a non negligible number
 of intra-individual polymorphic SNPs. Such observations could have several
 causes such as sequencing errors, the presence of heteroplasmy or transfer
 of chloroplast sequences in the nuclear and mitochondrial genomes. The
 occurrence of allelic diversity has practical important impacts on the
 identification of diversity, the analysis of the chloroplast data and
 beyond that, significant evolutionary questions. In this study, we show
 that the observed intra-individual polymorphism of chloroplast sequence
 data is probably the result of plastid DNA transferred into the
 mitochondrial and/or the nuclear genomes. We further assess nine different
 bioinformatics pipelines’ error rates for SNP and genotypes calling using
 SNPs identified in Sanger sequencing. Specific pipelines are adequate to
 deal with this issue, optimizing both specificity and sensitivity. Our
 results will allow a proper use of whole chloroplast NGS sequence and will
 allow a better handling of NGS chloroplast sequence diversity.
description: A571_Run4-TAG-10Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomeA571_Run4-R1-TAG-10.bamA571_Run7-TAG-9Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomeA571_Run7-R1-TAG-9.bamA571_RunHi-TAG-9Dioscorea abyssinica A571 sample - Whole genome sequencing (HiSeq) - .bam file containing reads after mapping on the chloroplast genomeA571_RunHi-R1-TAG-9.bamCR659_Run10-TAG-70Dioscorea rotundata CR659 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomeCR659_Run10-R1-TAG-70.bamP458_Run4-TAG-25Dioscorea praehensilis P458 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomeP458_Run4-R1-TAG-25.bamPa-Mayo9-R11T57_R1R2.fastqPodococcus acaulis Pa-Mayoko9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePa-Ndjo3-R11T18_R1R2.fastqPodococcus acaulis Pa-Ndjo3 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePa-Ndjo9-R11T16_R1R2.fastqPodococcus acaulis Pa-Ndjo9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePa-Ndjo11-R11T19_R1R2.fastqPodococcus barteri Pb-Ndjo11 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Aloum8-R11T73_R1R2.fastqPodococcus barteri Pb-Aloum8 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Campo1-R11T81_R1R2.fastqPodococcus barteri Pb-Campo1 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Kola5-R11T54_R1R2.fastqPodococcus barteri Pb-Kola5 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Oyem-R11T47_R1R2.fastqPodococcus barteri Pb-Oyem sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Podo5-1-R2T53_R1R2.fastqPodococcus barteri Podo 5-1 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomePb-Podo5-R11T79_R1R2.fastqPodococcus barteri Podo 5 sample - Long range PCR sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genomeTOG6208_mt_Run1-TAG-1O. glaberrima TOG6028 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_mt_Run1-TAG-6O. glaberrima TOG6028 sample - LR-PCR sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_mt_Run1-TAG-LRO. glaberrima TOG6028 sample - LR-PCR (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_nr_Run1-TAG-1O. glaberrima TOG6028 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_nr_Run1-TAG-6O. glaberrima TOG6028 sample - Chloroplast enrichment (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_nr_Run1-TAG-LRO. glaberrima TOG6028 sample - LR-PCR (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.TOG6208_cp_RUN1_TAG1O. glaberrima TOG6028 sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.TOG6208_cp_RUN1-TAG2-4_10-12.bamO. glaberrima TOG6028 sample - LRPCR library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.TOG6208_cp_RUN1-AG2-4_10-12.bamTOG6208_cp_RUN1_TAG6O. glaberrima TOG6028 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.PE08106-E1_cp_RUN5-TAG35Pennisetum glaucum PE08106-E1 sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN2_TAG32Pennisetum glaucum PE11356 sample - LRPCR library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN2_TAG11-20Dioscorea rotundata_CR629_sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN4_TAG-27RUN4_TAG28RUN4_TAG29RUN4_TAG24RUN4_TAG26RUN4_TAG-12.bamDioscorea praehensilis_P603_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN4_TAG25Dioscorea praehensilis_P458_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN4_TAG30Dioscorea praehensilis_A571_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.RUN3-TAG-55_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-55_R1_pairedRUN3-TAG-56_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-56_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN5-TAG35_R1_paired.fastqFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN5-TAG35_R2_paired.fastqFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-57_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-57_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-59_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-59_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-65_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-65_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-66_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-66_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-67_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-67_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-70_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-70_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsRUN3-TAG-55Pennisetum glaucum 18311 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-56Pennisetum glaucum 18945 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-57Pennisetum glaucum 19529 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-59Pennisetum glaucum 9024 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-65Pennisetum glaucum PE01514 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-66Pennisetum glaucum PE02747 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-67Pennisetum glaucum PE05720 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedRUN3-TAG-70Pennisetum glaucum PE05727 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were usedfiltcutRUN4-TAG-12_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-12_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-24_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-24_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-25_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-26_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-25_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-26_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-27_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-27_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-28_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-29_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-28_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-29_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-30_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-30_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-31_R1_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsfiltcutRUN4-TAG-31_R2_pairedFastq data : see sup. table 1 (MER-15-0195) for more detailsDioscorea_Bcfvcf produce when calling SNP on Dioscorea samples with Bcf methodDioscorea_Bcf_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Bcf methodDioscorea_BcfBvcf produce when calling SNP on Dioscorea samples with BcfB methodDioscorea_BcfB_A571vcf produce when calling SNP on Dioscorea abyssinica samples with BcfB methodDioscorea_BVar15vcf produce when calling SNP on Dioscorea samples with BVar15 methodDioscorea_BVar15_A571vcf produce when calling SNP on Dioscorea abyssinica samples with BVar15 methodDioscorea_BVar50vcf produce when calling SNP on Dioscorea samples with BVar50 methodDioscorea_BVar50_A571vcf produce when calling SNP on Dioscorea abyssinica samples with BVar50 methodDioscorea_Hapvcf produce when calling SNP on Dioscorea samples with Hap methodDioscorea_Hap_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Hap methodDioscorea_Univcf produce when calling SNP on Dioscorea samples with Uni methodDioscorea_Uni1vcf produce when calling SNP on Dioscorea samples with Uni1 methodDioscorea_Uni1_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Uni1 methodDioscorea_Uni_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Uni methodDioscorea_Var15vcf produce when calling SNP on Dioscorea samples with Var15 methodDioscorea_Var15_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Var15 methodDioscorea_Var50vcf produce when calling SNP on Dioscorea samples with Var50 methodDioscorea_Var50_A571vcf produce when calling SNP on Dioscorea abyssinica samples with Var50 methodSNP_mil_HET50-MINFREQ-15vcf produce when calling SNP on Pennisetum glaucum (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)SNP_PODO_HET50-MINFREQ-15vcf produce when calling SNP on Podoccocus ssp. (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)SNP_yam_HET50-MINFREQ-15vcf produce when calling SNP on Dioscorea (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)SNP_rice_HET50-MINFREQ-0n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0)SNP_rice_HET50-MINFREQ-5n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 5 )SNP_rice_HET50-MINFREQ-10n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 10)SNP_rice_HET50-MINFREQ-15n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 15 )