@article{fdi:010066166,
  title = {{I}ntra-individual polymorphism in chloroplasts from {NGS} data : where does it come from and how to handle it ?},
  author = {{S}carcelli, {N}ora and {M}ariac, {C}{\'e}dric and {C}ouvreur, {T}homas and {F}aye, {A}. and {R}ichard, {D}. and {S}abot, {F}ran{\c{c}}ois and {B}erthouly, {C}{\'e}cile and {V}igouroux, {Y}ves},
  editor = {},
  language = {{ENG}},
  abstract = {{N}ext-generation sequencing allows access to a large quantity of genomic data. {I}n plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. {E}ven though the chloroplast is a haploid organelle, {NGS} plastome data identified a nonnegligible number of intra-individual polymorphic {SNP}s. {S}uch observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. {T}he 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. {I}n 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. {W}e further assess nine different bioinformatics pipelines' error rates for {SNP} and genotypes calling using {SNP}s identified in {S}anger sequencing. {S}pecific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. {O}ur results will allow a proper use of whole chloroplast {NGS} sequence and will allow a better handling of {NGS} chloroplast sequence diversity.},
  keywords = {{C}hloroplast ; gatk ; intra-individual polymorphism ; {NGS} ; samtools ; {SNP}},
  booktitle = {},
  journal = {{M}olecular {E}cology {R}esources},
  volume = {16},
  numero = {2},
  pages = {434--445},
  ISSN = {1755-098{X}},
  year = {2016},
  DOI = {10.1111/1755-0998.12462},
  URL = {https://www.documentation.ird.fr/hor/fdi:010066166},
}