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. Banana streak virus (BSV) is one of the most important viruses infecting bananas. Banana endogenous virus sequences (BEVs) from badnavirus ancestors are widely present in various bananas. However, the determinants of genetic variation of BEVs are poorly understood. To elucidate the genetic diversity of BEVs, we obtained hundreds of BEVs from different bananas. These BEVs were belonged to Clade II and divided into 26 different BEVs groups. Ten 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 of nucleotide diversity, 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 populations were the most variable, while BEV GZ20 populations were the most conserved, suggesting that different BEVs populations had different evolutionary rates. Purifying selection, evolutionary rate, and base transition contributed to genetic variation of BEVs populations. Additionally, two recombination events were found in BEV GZ6 populations. This study provided a theoretical basis for further research on the functions and integration mechanisms of BEVs.