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Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing

Artikel i vetenskaplig tidskrift
Författare Filipe de Sousa
Yann Bertrand
Stephan Nylinder
Bengt Oxelman
Jonna S. Eriksson
Bernard E. Pfeil
Publicerad i PLoS ONE
Volym 9
Nummer/häfte 10
ISSN 1932-6203
Publiceringsår 2014
Publicerad vid Institutionen för biologi och miljövetenskap
Språk en
Länkar doi.org/10.1371/journal.pone.010970...
Ämnesord sequence capture, low-copy nuclear genes, substitution rates, phylogenetics, Medicago, legume family
Ämneskategorier Bioinformatik (beräkningsbiologi), Botanik, Genetik, Biologisk systematik

Sammanfattning

Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.

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