Mtgenome annotation and characteristics analysis
The rough annotation of protein-coding genes (PCGs), transfer RNA genes
(tRNAs), ribosomal RNA genes (rRNAs), and CR was initially identified
using MITOS (http://mitos.bioinf.uni-leipzig.de/index.py) (Berntet al. , 2013), and then determined in comparison of published
homologous mtgenome sequences in phylogeny-close species using MEGAX
(Kumar et al. , 2018). The tRNAs secondary structures were
predicted using tRNAscan-SE Search Server v. 1.21
(http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe & Eddy, 1997). The
annotation of the mtgenomes was corrected manually using the Geneious v.
4.8.5 (Kearse et al. , 2012), and final mtgenomes were submitted
to the GenBank database. The secondary structures of the tRNAs were
visualized and manually edited using VARNA (http://varna.lri.fr) (Dartyet al. , 2009). The mtgenomes were visualized using the Chloroplot
online server with default parameters (Zheng et al. , 2020). Base
composition and relative synonymous codon usage (RSCU) of 90 species of
mtgenome were computed with PhyloSuite desktop platform (Zhang et
al. , 2020). AT-skew [(A - T) / (A + T)] and GC-skew [(G - C) / (G
+ C)] were estimated to investigate nucleotide composition bias (Perna
& Kocher, 1995), and three-dimensional scatterplots of AT-Skew, GC-Skew
and AT% were drawn using Origin Pro v. 9.0 (Mikrajuddin and
Khairurrijal, 2009). Selection pressure of the 13 PCGs was analyzed by
calculating Ka (non-synonymous mutation rates) and Ks (synonymous
mutation rates) values with DnaSP v. 5.0 (Librado & Rozas, 2009), and
visualized using RStudio. Sequences saturation was assessed in DAMBE v.
5.0 (Xia, 2013).