… We designed primers for these sequences in Geneious Prime with the following … We also
extracted the IR, LSC, and SSC regions of each Pleurothallidinae plastome using Geneious …

… For the library preparation 1.6 μg sheared genomic DNA was used (Ligation Sequencing
Kit… Gene annotation and visualization were performed in Geneious Prime 2021.1. The yellow …

… The control regions from the complete mitogenomes were then extracted from the alignment
using Geneious and re-aligned with the other 41 CRs via MAFFT. An alignment with only …

… The cells contained numerous large (up to 1.6 μm), darkly stained elliptical organelles that …
, and 5.8S rRNA sequences were aligned with MUSCLE and edited manually in Geneious R9…

… using the MAFFT [37] algorithm in Geneious Prime 2021.1.1. Strand asymmetry was … by
DnaSP v6.12.03 [41]. The structure maps of mitogenomes were visualized using Geneious Prime …

… The annotation of the mitogenomes was corrected manually using the Geneious v 4.8.5 [39]…
ML analysis was performed using IQ tree ver.1.6.8 under edge-linked partition model with …

… , and calculating genome architecture was done primarily using CLC Genomics Workbench
v6.0.5 (CLC Bio) and Geneious Pro v6.1.6 (Biomatters) packages. Parameters for de novo …

… the BBDuk trimmer in Geneious with the minimum quality set … have been imported into
Geneious and further assembled … boundaries manually corrected in Geneious. The boundaries of …

… The visualization of the complete mitogenome structure was conducted by Geneious
Prime 2022.1.1. MEGA 6.0 (Tamura et al., 2013) was employed to compute the nucleotide …

… and Nanopore were further processed and analyzed in Geneious Prime (v2023.2.1) for
both … sequencing data against the complete CPV1 genome in Geneious Prime (v2023.2.1). …