Chromosome‐scale genome assembly of the autoalloenneaploid Arundo donax

Abstract Background Arundo donax L. has great potential as an energy crop due to its high biomass yield and broad adaptability, while lack of a reference genome is a hindrance to genetic improvement efforts for this species. Methods Genome assembly of A. donax was conducted by utilizing PacBio SMRT sequencing and high‐throughput chromosome conformation capture technology, with further analysis exploring the plant's ploidy, whole‐genome duplication event, and evolutionary history through comparative genomics. Results The genome assembly of A. donax consists of 1.30 Gb with a contig N50 size of 33.15 Mb. A total of 74 403 gene models were identified, with over 90% of genes being functionally annotated. Karyotype and synteny analyses revealed that A. donax is an autoalloenneaploid (3 n = 9 x = 108) and has experienced significant gene family expansion and two whole‐genome duplication events during its evolutionary history. Furthermore, utilizing the genome assembly, a variety of salinity stress‐related genes were uncovered through the analysis of public RNA‐seq data. Conclusions This study presents the initial chromosome‐scale genome assembly of A. donax , which will advance genetic comprehension and support the genetic enhancement of this important energy crop.