Tao Si-Qi, Cao Bin, Tian Cheng-Ming, Liang Ying-Mei
The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
Museum of Beijing Forestry University, Beijing, 100083, China.
BMC Genomics. 2017 Aug 23;18(1):651. doi: 10.1186/s12864-017-4059-x.
Rust 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.
The 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.
This 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.
锈菌是植物真菌病原体中最大的类群。然而，包括基因组序列、转录组序列和相关分子标记在内的数据匮乏，阻碍了抑制性化合物的开发，并妨碍了从进化角度对它们进行分析。山田胶锈菌和亚洲胶锈菌是两个密切相关的锈菌物种，它们分别是导致苹果锈病和梨锈病的具有生态和经济重要性的病原体，对果园具有毁灭性影响。在本研究中，我们调查了这两种胶锈菌在其生命周期的冬孢子阶段的转录组。本研究的目的是了解这两种相关真菌的进化模式，并鉴定通过选择而进化的基因。
山田胶锈菌和亚洲胶锈菌的转录组是从每个物种的三个生物学重复的RNA混合物中生成的。我们分别获得了山田胶锈菌和亚洲胶锈菌的49318和54742条转录本，N50值分别为1957和1664。我们还鉴定了一系列与致病性相关的候选效应子和其他基因家族。在这两个物种之间总共鉴定出4947对假定的直系同源物。对这些直系同源物的非同义/同义替换率比值的估计确定了116对Ka/Ks值大于1且处于正选择下的基因对，以及170对Ka/Ks值为1且处于中性选择下的基因对，而其余4661个基因则受到纯化选择。我们估计这两个物种之间的分歧时间约为520万年前。
本研究构成了对两种锈菌山田胶锈菌和亚洲胶锈菌转录组的从头组装和比较分析。结果鉴定出几个直系同源基因，并通过注释鉴定出许多表达基因。我们对Ka/Ks比值的分析鉴定出了经历正选择或纯化选择的直系同源基因。对这两个物种的进化分析提供了一个相对精确的分歧时间。总体而言，本研究获得的信息增加了可用于胶锈菌属遗传多样性研究的遗传资源。
