Chromosome-scale Genome Assembly of the Alloenneaploid Arundo donax

Abstract

Arundo donax L (A. donax). is a promising energy crop with high biomass and wide adaptability, while lack of reference genome limiting the genetic improvement of this crop. Here, we report the first chromosome-scale assembly of A. donax genome using Pacbio SMRT sequencing and Hi-C technology. The genome size of this assembly is 1.30 Gb with contig N50 33.15 Mb. A total of 74,403 gene models were predicted, of which over 90% of genes were functionally annotated. Karyotype analysis and synteny analysis revealed that A. donaxis an alloenneaploid (3n = 9x = 108). Comparative genome analysis indicated that A. donax has undergone strong gene family expansion and two whole-genome duplication events during evolution. Based on the genome assembly, we mined numerous salinity stress related genes using public RNA-seq data. The genome assembly we provided in this study will enhance genetic understanding and promote the genetic improvement of A. donax.