Complete mitogenome of Plagiognathops microlepis and its phylogenetic position within the subfamily Xenocyprinae (Cypriniformes: Cyprinidae)

Abstract

The complete mitochondrial genome of Plagiognathops microlepis was sequenced using Illumina NovaSeq and PacBio Sequel II platforms.The circular mitogenome is 16,632 bp in length and contains 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region (D-loop). The genome exhibits an AT content of 56.7%, with an AT skew of 0.104 and a GC skew of −0.255. COX1 initiates with GTG and CYTB with ATA, whereas the remaining 11 PCGs employ ATG; four PCGs (COX2, COX3, ND3, and ND4) terminate with incomplete stop codons (T or TA). Relative synonymous codon usage (RSCU) analysis revealed 27 preferred codons (RSCU > 1), with a strong bias toward A- and T-ending codons. All 22 tRNAs display conventional cloverleaf secondary structures. Maximum likelihood (ML), Bayesian inference (BI) and Neighbor joining (NJ) analyses consistently recovered P. microlepis as sister species to Xenocypris davidi (NJ bootstrap = 1, ML UFBoot = 67, BI posterior probability = 0.977), confirming its phylogenetic position within the genus Xenocypris. These findings provide molecular evidence for the taxonomic placement of P. microlepis and genomic resources for species delimitation, conservation genetics and evolutionary studies within Xenocyprinae.