@article{fdi:010092082,
  title = {{A}n {INDEL} genomic approach to explore population diversity of phytoplankton},
  author = {{D}evic, {M}. and {D}ennu, {L}. and {L}ozano, {J}. {C}. and {M}ariac, {C}{\'e}dric and {V}erg{\'e}, {V}. and {S}chatt, {P}. and {B}ouget, {F}. {Y}. and {S}abot, {F}ran{\c{c}}ois},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground{A}lthough metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. {T}his is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.{R}esults{T}o gain insight into population diversity, a novel method based on {INDEL} markers was developed on {B}athycoccus prasinos ({M}amiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. {L}ong read sequencing was first used to characterize structural variants among the genomes of six {B}. prasinos strains sampled from geographically distinct regions in the world ocean. {M}arkers derived from identified insertions/deletions were validated by {PCR} then used to genotype 55 {B}. prasinos strains isolated during the winter bloom 2018-2019 in the bay of {B}anyuls-sur-{M}er ({M}editerranean {S}ea, {F}rance). {T}his led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of {B}. prasinos. {F}inally, selected markers were directly tracked on environmental {DNA} sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.{C}onclusions{T}his method, which involves (i) pre-identifying the genetic diversity of {B}. prasinos in environmental samples by {PCR}, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of {B}. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in {B}. prasinos but also potentially in other generalist phytoplankton species.},
  keywords = {{P}hytoplankton ; {B}athycoccus ; {I}ntraspecific diversity ; {G}enotyping ; {B}loom ; {MEDITERRANEE} ; {FRANCE} ; {MONDE}},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {25},
  numero = {1},
  pages = {1045 [13 ]},
  ISSN = {1471-2164},
  year = {2024},
  DOI = {10.1186/s12864-024-10896-w},
  URL = {https://www.documentation.ird.fr/hor/fdi:010092082},
}