Assembly, annotation, and analysis

Getorganells splicing software (https://github.com/Kinggerm/GetOrganelle) was used to splice the sequenced reads in multiple iterations, and the initial assembly results were obtained. Then, the clean reads were compared back to the mitochondrial genome sequence, and the bases were corrected using Pilon v1.23 (Walker et al. 2014) and annotated using MITOS2 (http://mitos2.bioinf.uni-leipzig.de/index.py) (Ren et al. 2020). The mitochondrial circle mapping was done by OGDRAW (https://chlorobox.mpimp-golm.mpg.de/O).

GDraw.html). In order to explore the phylogenetic position of N. soroides, we used the whole mitochondrial data from the nucleotide and performed multiple sequence alignments. After multiple sequence alignments, a phylogenetic tree by MEGA 7.0 (Kumar et al. 2016) was generated, using maximum likelihood (ML) to performe phylogenetic analysis, and generated 1000 bootstraps. The phylogenetic trees in this study include 24 fish species belonging to Neolissochilus, Tor, Acorssocheilus, and Puntius (as an outgroup).