Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum)

Si-Qi Tao,Cheng-Ming Tian,Bin Cao,Ying-Mei Liang

doi:10.1186/s12864-017-4059-x

Abstract

BackgroundRust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. In this study, we investigated the transcriptomes of these two Gymnosporangium species during the telial stage of their lifecycles. The aim of this study was to understand the evolutionary patterns of these two related fungi and to identify genes that developed by selection.ResultsThe transcriptomes of G. yamadae and G. asiaticum were generated from a mixture of RNA from three biological replicates of each species. We obtained 49,318 and 54,742 transcripts, with N50 values of 1957 and 1664, for G. yamadae and G. asiaticum, respectively. We also identified a repertoire of candidate effectors and other gene families associated with pathogenicity. A total of 4947 pairs of putative orthologues between the two species were identified. Estimation of the non-synonymous/synonymous substitution rate ratios for these orthologues identified 116 pairs with Ka/Ks values greater than1 that are under positive selection and 170 pairs with Ka/Ks values of 1 that are under neutral selection, whereas the remaining 4661 genes are subjected to purifying selection. We estimate that the divergence time between the two species is approximately 5.2 Mya.ConclusionThis study constitutes a de novo assembly and comparative analysis between the transcriptomes of the two rust species G. yamadae and G. asiaticum. The results identified several orthologous genes, and many expressed genes were identified by annotation. Our analysis of Ka/Ks ratios identified orthologous genes subjected to positive or purifying selection. An evolutionary analysis of these two species provided a relatively precise divergence time. Overall, the information obtained in this study increases the genetic resources available for research on the genetic diversity of the Gymnosporangium genus.

Highlights

Rust fungi constitute the largest group of plant fungal pathogens
About one month after the teliospores began to extrude from galls macroscopically, three biological replicates were collected for each species
To gain further insight into the physiological and molecular factors playing a role in the telial stage, we focused on several gene families shared between G. yamadae and G. asiaticum based on functional annotations

Summary

Introduction

Rust fungi constitute the largest group of plant fungal pathogens. a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. G. yamadae Miyabe ex Yamada and G. asiaticum Miyabe ex Yamada are difficult to distinguish in the wild, and both are economically important species for apple and pear production and for cultivated Junipers in Asia. Rust diseases caused by Gymnosporangium species on apple and pear trees (Fig. 1a and b), which commonly occur in many provinces, threaten economic orchard development [5, 6]. As landscape trees, junipers have been widely planted in places such as parks, districts, and graveyards; the strange appearance and bright colour of the telial horns of Juniperus plants has caused much concern because their aesthetic value is impacted by rust fungi (Fig. 1c and d). Rust fungal infections cause stem swelling and deformed branches, occasionally resulting in branch knots that can kill the tree hosts

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