@article{fdi:010091391,
  title = {{T}ruly the best of both worlds : merging lineage-specific and universal probe kits to maximize phylogenomic inference},
  author = {{F}onseca, {L}. {H}. {M}. and {A}sselman, {P}. and {G}oodrich, {K}. {R}. and {N}ge, {F}. {J}. and {S}oule, {V}incent and {M}ercier, {K}. and {C}ouvreur, {T}homas and {C}hatrou, {L}. {W}.},
  editor = {},
  language = {{ENG}},
  abstract = {{P}remise: {H}ybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade-specific kits available. {H}ere, we present a probe kit targeting 799 low-copy - copy genes for the plant family {A}nnonaceae. {M}ethods: {T}his new version of the kit combines the original 469 genes from the previous {A}nnonaceae kit with 334 genes from the universal {A}ngiosperms353 kit. {W}e also compare the results obtained using the original {A}ngiosperms353 kit with our custom approach using a subset of specimens. {P}arsimony-informative - informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera {A}simina and {D}eeringothamnus. {R}esults: {T}he {A}nnonaceae799 genes derived from the {A}ngiosperms353 kit have extremely high recovery rates. {O}ff-target reads were also detected. {W}hen evaluating size, the proportion of on- and off-target regions, and the number of parsimony- informative sites, the genes incorporated from the {A}ngiosperms353 panel generally outperformed the genes from the original {A}nnonaceae probe kit. {D}iscussion: {W}e demonstrated that the new sequences from the {A}ngiosperms353 probe set are variable and relevant for future studies on species-level - level phylogenomics and within-species - species studies in the {A}nnonaceae. {T}he integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies.},
  keywords = {{A}ngiosperms353 ; {A}nnonaceae ; {A}simina ; bait set ; {D}eeringothamnus ; phylogenetics},
  booktitle = {},
  journal = {{A}pplications in {P}lant {S}ciences},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[13 p.]},
  ISSN = {2168-0450},
  year = {2024},
  DOI = {10.1002/aps3.11615},
  URL = {https://www.documentation.ird.fr/hor/fdi:010091391},
}