A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis

Abstract

Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

Insights from the first genome assembly of Onion (Allium cepa)

“…The completeness of the Dovetail scaffolded de novo genome assembly was evaluated using BUSCO genes (embryophyta_odb10; 2020-09-10; File S4) and resulted in a completeness score of 87.7%. Other large genome assemblies, such as the loblolly pine v1.01 genome has an CEGMA completeness of 91% (Neale et al 2014) and the Allium sativum v1.0 genome has an CEGMA completeness score of 92.7% and a BUSCO completeness score of 88.7% (Sun et al 2020). Of the BUSCO genes, 3.3% were labeled as fragmented, which could be because the length of the gene model did not fall within the expected length distribution of the chosen BUSCO profile.…”

“…This observation agrees with the observed Kmer statistics, which suggests that 53,8% of the genome is single copy and the observations by Jakše et al (2008) that onion BAC sequences contain > 50 % sequences that are like transposons, many of which are degraded. Using de novo repeat annotation strategies, genomes comparable in size, such as garlic (Sun et al 2020), bread wheat (Mayer et al 2014) and loblolly pine (Wegrzyn et al 2014) were annotated as containing approx. 91%, 80%, and 82% repetitive DNA sequences, respectively.…”

“…Synteny between A. cepa (onion) and A. sativum (garlic) Onion EST based markers (Shigyo 2020) were also used to study the synteny between onion and garlic (Sun et al 2020). For 3,123 markers out of the 4,340, physical positions were determined on both the garlic and onion chromosomes.…”

Genome Survey Sequencing of Nomocharis forrestii, Assembly of Its Complete Chloroplast Genome and Analysis of Simple Sequence Repeat (SSR) Markers

“…The genome of garlic, a member of the Liliaceae family, has been reported previously. The size of the sequenced garlic genome is 16.24 Gb, accounting for 96.1% of the total garlic genome [29] .…”

Parallel analysis of global garlic gene expression and alliin content following leaf wounding

“…The diploid genome of garlic (2n = 2x = 16) is estimated to be 15.9G, 32 times the size of the rice genome. Liu [35] recently reported the genome assembly of garlic at the chromosome level, making it the rst species within the Allium genus to be sequenced. According to these sequencing results, garlic experienced a recent occurrence of transposable elements, which helps explain the evolution of allicin biosynthesis-related genes.…”