Integration of Illumina and PacBio HiFi Sequencing Reveals a Three-Linear-Molecule Mitogenome with RNA-Editing Sites and Phylogeny in Arrow Bamboo (Fargesia qinlingensis)

Abstract

Arrow bamboo (Fargesia qinlingensis) is endemic to the Qinling Mountains and has remarkable adaptive resilience to changing climates. However, its complete mitogenome remains unknown. Using the Illumina and PacBio HiFi sequencing platforms, we found that the mitogenome assembly of the F. qinlingensis has a multi-branched skeleton comprising three linear molecules (M1, M2, and M3), with a length of 442,368 bp and a GC content of 44.05%. Thirty-five unique PCGs were identified in the complete mitogenome, including twenty-four core structural genes, eleven noncore structural genes, three rRNAs, and sixteen tRNAs. The GCU for alanine and CAA for glutamine represented the most significant frequency (RSCU = 1.55) in the codon usage preference. A total of 51, 28, and 14 SSRs were determined on M1, M2, and M3, respectively. The mitogenome contained 149 pairs of dispersed repeats with lengths greater than 30 bp, the most abundant of which were 82 forward and 67 palindromic repeats. A long repeat sequence (14,342 bp) was characterized in mediating mitogenome recombination. DNA transfer analyses suggested that 44 MTPTs (30,943 bp, 6.99%) originated from the plastome. Among the 482 potential C-U/T RNA-editing sites predicted in 35 PCGs, ccmFn (38 times) and ccmC (36 times) shoed the highest frequency. Collinearity and phylogenetic trees revealed the close relationship between F. qinlingensis and Bambusa oldhamii. The primary features of the mitogenome of F. qinlingensis will help decipher the functional mitochondrial traits related to growth performance and climate resilience. Moreover, our findings provide insights into the evolution, environmental adaptation, and sustainable use of subalpine bamboo resources in the Qinling Mountains.