Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parme
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IMA Fungus
RESEARCH
Open Access
Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) Felix Grewe1* , Claudio Ametrano1, Todd J. Widhelm1, Steven Leavitt2, Isabel Distefano1, Wetchasart Polyiam3, David Pizarro4, Mats Wedin5, Ana Crespo4, Pradeep K. Divakar4 and H. Thorsten Lumbsch1
Abstract Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenatedbased Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow. Keywords: Next-generation sequencing, Target capture, HybPiper, Phylogenomics, Maximum likelihood, Bayesian interference, ASTRAL, Parmotrema, Parmelioideae, Protoparmelioideae
INTRODUCTION Our understanding of evolutionary relationships of fungi at all phylogenetic levels has dramatically improved with the availability of genetic data from entire genomes following remarkable progress in sequencing technologies (Ametrano et al. 2019; Ebersberger et al. 2012; Robbertse et al. 2006; Spatafora et al. 2017). In addition to sequencing complete genomes, a number of more cost-efficient * Correspondence: [email protected] 1 Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA Full list of author information is available at the end of the article
methods have been developed to sample subsets of genome-scale data. These include several direct sequencing approaches, such as restriction site associated DNA sequencing (RADseq) (Andrews et al. 2016), or capture sequencing approaches using baits, such as target enrichment of specific genes (Bragg et al. 2016) or ultraconserved elements (Faircloth et al. 2
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