10.3390/ijms22189713 Phylogenetic Trees Study

Resource Type: 
Project
Name: 
10.3390/ijms22189713 Phylogenetic Trees Study
Short Description: 

This project provides two analyses for the two phylogenetic trees presented in figure 4 of the publication.

Publication: 
Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies.. International journal of molecular sciences. 2021 Sep 08; 22(18).
Analysis: 
NameDescription
10.3390/ijms22189713 Plastid phylogenetic tree
Phylogenetic relationships were inferred from 53 species of the Apiaceae family by using Panax notoginseng (Arialaceae) as an outgroup. The 54 plastid genomes were retrieved from GenBank and aligned using MAFFT v7.450 under default parameters; Geneious prime (Biomatters, Inc., San Diego, CA, USA) was used to reconstruct the phylogenetic relationships based on the Neighbor-Joining (NJ) method, and 1000 bootstrap replicates.
10.3390/ijms22189713 rbcL phylogenetic tree
Phylogenetic relationships were inferred from 53 species of the Apiaceae family by using Panax notoginseng (Arialaceae) as an outgroup. rbcL sequences were extracted from plastid genomes retrieved from GenBank and aligned using MAFFT v7.450; the phylogenetic relationships based on the Neighbor-Joining (NJ) method and 1000 bootstrap replicates were reconstructed using Geneious prime (Biomatters, Inc., San Diego, CA, USA) under default parameters.