Computational protocol: The Chemical and Genetic Characteristics of Szechuan Pepper (Zanthoxylum bungeanum and Z. armatum) Cultivars and Their Suitable Habitat

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Protocol publication

[…] A nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence possesses highly interspecific divergence and the capability to distinguish closely related taxa of medicinal plant at the species level (Chen et al., ). In this study, 119 specimens of Szechuan pepper cultivars and seven related species were sampled (Supplementary Table ). One sequence of Z. ovalifolium var. spinifolium was also downloaded from the GenBank database. DNA extraction, PCR amplification and sequencing were performed as previously described (Chen et al., ; Xin et al., ). Consensus sequences and coting generation were performed using CondonCode Aligner V 3.7.1 (CodonCode Co., Centreville, MA, USA). All of the ITS2 sequences were annotated with the Hidden Markov Model (HMM) (Wolf et al., ; Keller et al., ). The sequences were aligned using Muscle, the genetic distance computed by MEGA 6.0 (Center for Evolutionary Medicine and Informatics, Tempe, Arizona, USA) based on the K2P model (Tamura et al., ). A phylogenetic tree constructed by employing the neighbor-joining (NJ) tree method, and bootstrap tests were conducted by applying 1000 resamples to assess the confidence in phylogenetic analysis using MEGA 6.0. Three sequences of Toddalia asiatica downloaded from GenBank were chosen as outgroup when the NJ tree was built. […]

Pipeline specifications

Software tools MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Zanthoxylum bungeanum