Population genetic diversity analyses reveal the determinants of genetic variation of banana endogenous virus sequences in China

Banana (Musa spp.) is an economic crop in tropical and subtropical areas, especially in South China. However, banana streak virus (BSV) is a major constraint in banana production. Banana endogenous virus sequences (BEVs) from badnavirus ancestors are widely present in various bananas. The genetic variation of BEVs populations are poorly understood. To elucidate the genetic diversity of BEVs, we obtained 327 BEVs from different bananas. These BEVs belonged to Clade II and were divided into 26 different BEVs groups. Ten BEVs groups were chosen to analyze the genetic diversity of BEVs populations. The results revealed that each BEVs population had an Hd value of 1.0 and a Pi value of more than 0.005, indicating that there was a great genetic diversity among these BEVs populations. The analyses of genetic variation of various BEVs populations showed that BEV UF population was the most variable, while BEV GZ20 population was the most conserved, suggesting that different BEVs populations had different selection pressures. Furthermore, purifying selection and base transition contributed to genetic variation of BEVs populations. Additionally, two recombination events were found in BEV GZ6 populations and required further confirmation. This study provided a theoretical basis for further research on the functions and integration mechanisms of BEVs.