Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

• DOI: 10.1371/journal.pone.0139840
• Publication Date: 2015-10-02T18:00:55Z
• Authors: Luxian Liu; Xinjie Jin; Nan Chen; Xian Li; Pan Li; Chengxin Fu
• Keywords: Maximum parsimony

Phylogenetic relationships among Chinese species of Morella (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic rubra, M. adenophora, nana and esculenta. Three methods for inferring phylogeny, maximum parsimony (MP), likelihood (ML) Bayesian concordance, were applied data sets including as many 4253 RAD with 8360 informative variable sites. All three significantly favored the topology (((M. adenophora), nana), esculenta). Two from North America (M. cerifera pensylvanica) placed sister four species. According BEAST analysis, deduced speciation rubra be at about Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence occurred late Pliocene (3.39 From pooled data, assembled 29378, 21902 23552 de novo contigs an average length 229, 234 bp esculenta respectively. The used investigate functional classification tags a BLASTX search. Additionally, identified 3808 unlinked SNP sites across populations discovered genes associated fruit ripening senescence, quality disease/defense metabolism based on KEGG database.