biology Article Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci Chingchai Chaisiri 1,2,3 , Xiangyu Liu 1,2,3, Yang Lin 2,3 , Yanping Fu 2,3, Fuxing Zhu 3 and Chaoxi Luo 1,2,3,* 1 Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China;
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[email protected] Simple Summary: Diaporthe eres is one of the most serious plant pathogenic fungi that affect many economically important plants. It can cause rootstock death, stem canker, stem necrosis, dead branch, shoot blight, fruit rot, leaf spot, leaf necrosis, and umbel browning. In general, morphological and molecular characterization using multiple loci sequences were performed for the identification of Diaporthe species. However, there are morphological differences due to culture conditions, and the taxonomy of species of Diaporthe is unclear because the phylogeny based on different genes gives different tree topologies. In this study, we evaluate the phylogenetic relationships and population diversity among D. eres and other Diaporthe species. Our results showed that phylogenetic analyses Citation: Chaisiri, C.; Liu, X.; Lin, Y.; from concatenated multi-locus DNA sequence data could resolve the D.