Population structure and mitogenomic analyses reveal dispersal routes of Macrobrachium nipponense in China

The oriental river prawn Macrobrachium nipponense is widely distributed in China, but its origin and distribution routes remain largely unknown. We collected 126 oriental river prawn specimens from four lakes and one river across China, and sequenced their mitochondrial cytochrome C oxidase subunit I (cox1) genes. We performed whole-genome resequencing of 100 samples and assembled mitogenomes for population analysis, these two types of mitochondrial markers (cox1 and all 13 protein-coding genes-13 PCGs), a nuclear marker (28S rRNA) and SNPs to infer the relationships between the five populations, the population structure, and migratory routes. We also assembled complete mitogenome per sampled population (5 in total) and used them to conduct comparative mitogenomic analyses.

The complete mitogenomes comprised 15,774-15,784 base pairs (bp). The average nucleotide diversity (π) of the populations, inferred using the cox1 gene data, was 0.03013 ± 0.00618, ranging from 0.00500 ± 0.00110 (Fuxian Lake) to 0.03562 ± 0.02538 (Khanka Lake). The identified haplotypes (33 cox1 and 101 13 PCGs) clustered into three main geographical lineages. Lineage A included Khanka Lake and one clade from the Haihe River. The specimens from Fuxian Lake constituted lineage B. Lineage C comprised a majority of specimens from the Haihe River, Taihu Lake, and Poyang Lake, and a minority of specimens from Khanka Lake and Fuxian Lake.

This study indicates that native M. nipponense prawns in China originated from East China, subsequently spreading northward and westward into the inland regions along the Grand Canal and the Yangtze River system, forming distinct lineages. This proposed route improves our understanding of the geographic distribution and origin of M. nipponense in China.