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Comparative genome/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway.
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2019-11-15 , DOI: 10.1111/1755-0998.13104
Cheng-Yi Tang 1 , Song Li 1, 2 , Yun-Tong Wang 2 , Xi Wang 2
Affiliation  

Boraginales (the forget-me-not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single-copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O-acyl transferase.

中文翻译:

比较的基因组/转录组分析可探查Boraginales的系统发生位置,Boraginales中的WGD和链烷/紫草素核心途径中的关键酶基因。

Boraginales(勿忘我秩序)是lamiids进化枝中的核心群体。但是,到目前为止,还没有报道来自Boraginales的基因组,而且公开的转录组也很少见。在这里,我们报告了第一个Boraginales物种的新基因组(即Echium plantagineum基因组)和其他七个Boraginales物种的转录组,以探讨三个问题:(i)Boraginales在层状进化枝中的系统发生位置;(ii)牛羚体内潜在的全基因组重复(WGD);(iii)链烷/紫草素核心途径中的候选关键酶基因。结果表明:(i)至少基于基因组/转录组数据的单拷贝直系同源基因,牛肝菌最有可能比拉米亚斯更靠近茄属/龙胆属。(ii)在伽玛(γ)事件之后,紫草科(分类为Boraginales I进化枝)可能至少经历了两轮WGD,而Heliotropiaceae和Ehretiaceae(分类为Boraginales II进化枝)可能仅经历了一轮WGD。(iii)推断了链烷宁/紫草素核心途径中的几个候选关键酶基因,例如,与香叶基环化酶,萘酚羟化酶和O-酰基转移酶相对应的基因。
更新日期:2019-11-15
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