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 (3n = 9x = 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.

Keywords

Arundo donax / autoallopolyploid / comparative genomics / genome assembly

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