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To investigate the population structure and phylogenetic relationships among different geographic populations of Asiatic rice borer Chilo suppressalis in Ningbo City, China,whole-genome resequencing was performed on 37 individuals from eight populations (six from Ningbo, one from Beijing, and one from Hangzhou). Genomic variations were identified, and population genetic analyses including population structure, selective sweeps, genetic diversity, and historical effective population size were conducted. The results showed that a total of 42 149 215 single nucleotide polymorphisms and 11 912 812 insertions/deletions were identified across the 37 genomes, with most variations located in intergenic and intronic regions. Among the six Ningbo populations, Yinzhou, Yuyao and Haishu populations were closely related, whereas the Xiangshan population showed the greatest genetic distance from the other Ningbo populations and exhibited moderate genetic differentiation. Genes within the selective sweep regions of the Xiangshan population was significantly enriched in seven signaling pathways, including melanogenesis and circadian entrainment. Among the Ningbo populations, nucleotide diversity was relatively higher in the Haishu and Yinzhou populations, but lower in the Xiangshan and Fenghua populations. The Ningbo populations experienced a rapid contraction approximately 3 000—1 000 years ago, followed by a rapid population expansion.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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