Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach.
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3' untranslated regions (3'-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3'-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3'-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3'-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.
Université Montpellier 2, CNRS, Institut des Sciences de l'Évolution (UMR 5554), Place Eugène Bataillon, 34095 Montpellier cedex 05, France. Electronic address: jeanne.tonnabel@univ-montp2.fr.
Jeanne
J
Tonnabel
Isabelle
I
Olivieri
Agnès
A
Mignot
Anthony
A
Rebelo
Fabienne
F
Justy
Sylvain
S
Santoni
Stéfanie
S
Caroli
Laure
L
Sauné
Olivier
O
Bouchez
Emmanuel J P
EJ
Douzery
D002467:Cell Nucleus / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D011110:Polymorphism, Genetic; D039105:Proteaceae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
D018744:DNA, Plant; D005819:Genetic Markers
3′-UTR; Non-models groups; Orthology; Phylogenetic markers; Proteaceae; RNA-seq