Molecular identification and adaptive evolution analysis of Juncao in Arundo

Although methods for the morphological identification of Juncao in Arundo have been established, research on it at the molecular level is lacking. Molecular identification and selection pressure analysis of Juncao in Arundo can lay the foundation for future hybrid breeding of Juncao. In this study, the ITS2 gene sequences of Juncao in Arundo were obtained by PCR amplification, and the transcriptomes of the leaves were sequenced. Molecular identification and selection pressure analyses were performed using bioinformatics methods. The results showed that two large-scale differentiations occurred, 6.21 million years－9.75 million years ago and 5.14 million years－8.07 million years ago. They were divided into three clades: LZ_No.3, LZ_No.5, LZ_No.6, LZ_No.8, and LZ_No.2, LZ_No.4, LZ_No.7, LZ_No.12, and other Juncao. Selection pressure analysis screened out the positively selected genes of LZ_No.1 and LZ_No.3, most of which were related to transcriptional regulation, stress resistance, and development. The results revealed the relationship between Juncao in Arundo and the genes and loci subjected to positive selection, providing insights into the adaptive evolution of Juncao in Arundo and offering targets for future genetic improvement.