@article{fdi:010074890,
  title = {{P}hylogenomics of the major tropical plant family {A}nnonaceae using targeted enrichment of nuclear genes},
  author = {{C}ouvreur, {T}homas and {H}elmstetter, {A}. {J}. and {K}oenen, {E}. {J}. {M}. and {B}ethune, {K}{\'e}vin and {B}randao, {R}. {D}. and {L}ittle, {S}. {A}. and {S}auquet, {H}. and {E}rkens, {R}. {H}. {J}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}argeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. {A}nnonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. {B}aits were designed by sequencing the transcriptomes of five species from two of the largest {A}nnonaceae subfamilies. {O}rthologous loci were identified. {T}he resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide {A}nnonaceae analysis sampling 65 genera and a species level analysis of tribe {P}iptostigmateae sampling 29 species with multiple individuals per species. {DNA} extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. {O}ur kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across {A}nnonaceae. {S}ilicagel dried and herbarium {DNA} worked equally well. {W}e present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. {R}esults mainly confirm previous chloroplast based studies. {H}owever, several new relationships are found and discussed. {W}e show significant differences in branch lengths between the two large subfamilies {A}nnonoideae and {M}almeoideae. {A} new tribe, {A}nnickieae, is erected containing a single {A}frican genus {A}nnickia. {W}e also reconstructed a well-resolved species-level phylogenetic tree of the {P}iptostigmteae tribe. {O}ur baiting kit is useful for reconstructing well-supported phylogenetic relationships within {A}nnonaceae at different taxonomic levels. {T}he nuclear genome is mainly concordant with plastome information with a few exceptions. {M}oreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal {DNA} as previously shown. {O}ur results have implications for understanding the biogeography, molecular dating and evolution of {A}nnonaceae.},
  keywords = {{A}nnonaceae ; rain forests ; systematics ; transcriptomes ; {P}iptostigmateae ; herbarium ; {ZONE} {TROPICALE}},
  booktitle = {},
  journal = {{F}rontiers in {P}lant {S}cience},
  volume = {9},
  numero = {},
  pages = {1941 [15 ]},
  ISSN = {1664-462{X}},
  year = {2019},
  DOI = {10.3389/fpls.2018.01941},
  URL = {https://www.documentation.ird.fr/hor/fdi:010074890},
}