Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

Abstract

Background: Armillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.

Results: The de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.

Conclusions: These characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.

Keywords: Armillaria; Gastrodia elata; Genome; Molecular mechanism; Symbionts.

Fig. 1

GO functional annotation of the A. gallica Jzi34 genome. GO annotation is divided into three major categories and 47 subclasses. A different colour represents each subclass. The x-axis represents the class of genes and the y-axis represents the percent of genes (%). The z-axis represents the number of genes

Fig. 2

KEGG pathway annotation of the A. gallica Jzi34 genome. KEGG pathway annotation is divided into six major classes and 45 subclasses. The x-axis indicates the gene number of the concerned subclass. Each subclass is represented by a different colour

Fig. 3

KOG functional annotation of proteins in the A. gallica Jzi34 genome. KOG function classification is summarized in 26 classes. The x-axis indicates each class and the y-axis shows the number of matched genes. The names of groups and number of genes are mentioned

Fig. 4

Carbohydrate enzyme functional classification. The CAZy classification is divided into 6 classes, including AA, CBM, CE, GH, GT and PL. The x-axis shows the CAZy class and the y-axis indicates the number of genes

Fig. 5

Functional classification of cytochrome P450 in the A. gallica Jzi34 genome. cytochrome P450 annotation is divided into 12 classes. The x-axis represents the P450 class. The y-axis represents the number of matched genes

Fig. 6

PHI classification in the A. gallica Jzi34 genome. PHI annotation is classified into 8 classes. The x -axis shows each class, and the y-axis represents the number of matched genes

Fig. 7

Syntenic analysis of P450 genes between A.gallica Jzi34 and four other Armillaria. The gray lines at the bottom indicate the collinear blocks within A.gallicaJzi34 and other Armillaria genomes. The red lines indicate the pairs of P450 genes. The results of the syntenic analysis between A.gallica Jzi34 and other Armillaria, including A. cepistipes B5, A. gallicaAr21-2, A. ostoyae C18/9, and A. solidipes 28-4 (A–D)