Mitogenomic Architecture and Phylogenetic Insights Shed Light on the Matrilineal Evolution of the Mahseer Fish Neolissochilus sumatranus (Cyprinidae: Torinae) in Southeast Asia.

The systematics and sustainable fisheries management of Neolissochilus sumatranus (Weber and de Beaufort 1916) remain challenging due to taxonomic controversies and limited molecular data. Hence, this study utilized next-generation sequencing to generate a mitogenome of N. sumatranus, morphologically identified from northern Sumatra, Indonesia. The assembled mitogenome of this species is 16,584 bp long and consists of 37 genes and a control region (CR). The comparative analysis with nine other Neolissochilus species revealed a highly conserved genetic organization, with relative synonymous codon usage showing high frequencies for arginine, leucine, and serine. Most protein-coding genes (PCGs) in N. sumatranus used ATG as the initiation codon, a pattern widely observed in vertebrate mitogenomes. Conversely, incomplete stop codons (TA- and T-) are proposed to be completed post-transcriptionally through polyadenylation during mRNA maturation. The nonsynonymous-to-synonymous substitution ratios were below '1' for 12 PCGs, except Cytb in Neolissochilus species, indicating that the majority of these genes are subject to purifying selection. The secondary structures of all 22 transfer RNAs in N. sumatranus retained the canonical cloverleaf configuration, displaying no reduction of the dihydrouridine arm typically observed in tRNA-Ser1, thereby reflecting structural variation within cyprinids. The comparative assessment of the CR among Neolissochilus species demonstrated four conserved sequence blocks (CSB-D, CSB-1, CSB-2, and CSB-3) exhibiting species-specific variation, while the tandem repeats were detected in only six of the eight analyzed species. These non-coding regions also exhibited differences in length and nucleotide composition among the examined Neolissochilus species, highlighting their utility for comparative genetic studies. However, their applicability as population-level markers remains to be evaluated using multiple specimens per species to capture intraspecific variation. The mitogenome-based phylogenetic inference corroborates the monophyly of Torinae and suggests a close evolutionary relationship among N. sumatranus, N. hendersoni, and N. soroides, which may be associated with their shared biogeographic history in the Sundaland region. The cladistic relationships between the genera Neolissochilus and Tor remain poorly resolved, with Neolissochilus benasi and Tor remadevii potentially constituting distinct lineages outside the core Neolissochilus and Tor clades, respectively. The phylogenetic positions of Tor douronensis and T. tambra are inconsistent despite their taxonomic synonymy, emphasizing the need for morpho-genetic studies across mainland and island Southeast Asian populations. Overall, the novel mitogenome of N. sumatranus clarifies its phylogenetic position within Torinae and provides a foundation for future systematics study.