Jason R Comer1, Wendy B Zomlefer1, Craig F Barrett2, Jerrold I Davis3, Dennis Wm Stevenson4, Karolina Heyduk1, James H Leebens-Mack1. 1. University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA. 2. California State University, Los Angeles, Department of Biological Sciences, Los Angeles, California 90032-8201 USA. 3. Cornell University, Department of Plant Biology, Ithaca, New York 14853-4301 USA. 4. New York Botanical Garden, Bronx, New York 10458-5126 USA.
Abstract
PREMISE OF THE STUDY: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. METHODS: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. KEY RESULTS: Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. CONCLUSIONS: The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.
PREMISE OF THE STUDY: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. METHODS: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. KEY RESULTS: Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. CONCLUSIONS: The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.
Authors: Amanda de Santana Lopes; Túlio Gomes Pacheco; Odyone Nascimento da Silva; Leila do Nascimento Vieira; Miguel Pedro Guerra; Eduardo Pacca Luna Mattar; Valter Antonio de Baura; Eduardo Balsanelli; Emanuel Maltempi de Souza; Fábio de Oliveira Pedrosa; Marcelo Rogalski Journal: Plant Mol Biol Date: 2021-01-01 Impact factor: 4.076
Authors: Jason R Comer; Wendy B Zomlefer; Craig F Barrett; Dennis Wm Stevenson; Karolina Heyduk; James H Leebens-Mack Journal: Data Brief Date: 2016-03-02
Authors: Oriane Loiseau; Ingrid Olivares; Margot Paris; Marylaure de La Harpe; Anna Weigand; Darina Koubínová; Jonathan Rolland; Christine D Bacon; Henrik Balslev; Finn Borchsenius; Angela Cano; Thomas L P Couvreur; César Delnatte; Frédérique Fardin; Marc Gayot; Fabian Mejía; Talita Mota-Machado; Mathieu Perret; Julissa Roncal; Maria José Sanin; Fred Stauffer; Christian Lexer; Michael Kessler; Nicolas Salamin Journal: Front Plant Sci Date: 2019-07-12 Impact factor: 5.753