Data from: Pinpointing genes underlying annual/perennial transitions with comparative genomics

Background

Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella).

Results

After sorting all genes in all nine species into gene families, we identified five families in which well-annotated genes are present in the perennials A. lyrata and A. alpina, but are not present in any of the annual species. For the eleven genes in perennials in these families, an orthologous pseudogene or otherwise highly diverged gene was found in the syntenic region of the annual species in six cases. The five candidate families identified encode: a kinase, an oxidoreductase, a lactoylglutathione lyase, a F-box protein and a zinc finger protein. By comparing the active gene in the perennial to the pseudogene or heavily altered gene in the annual, dN and dS were calculated. The low dN/dS values in one kinase suggest that it became pseudogenized more recently, while the other kinase, F-box, oxidoreductase and zinc-finger became pseudogenized closer to the divergence between the annual-perennial pair.

Conclusions

We identified five gene families that may be involved in the life history switch from perennial to annual. Considering the dN and dS data and whether syntenic pseudogenes were found and the potential functions of the genes, the F-box family is considered the most promising candidate for future functional studies to determine if it affects life history.

研究背景
多年生与一年生生活史的转换在植物演化支中频繁发生，但调控植物为一年生或多年生的核心基因仍尚未明确。为鉴定赋予一年生与多年生植物差异的基因，我们对十字花科（Brassicaceae）中的4对姊妹演化支的基因含量进行了比较。每对演化支均包含1个一年生物种和1个多年生物种，此外还纳入了1个额外的一年生物种红花荠（Capsella rubella）。这4对姊妹演化支分别为：拟南芥（Arabidopsis thaliana）/ lyrata鼠耳芥（Arabidopsis lyrata）、蒙布特山芥（Arabis montbretiana）/ 高山山芥（Arabis alpina）、春山芥（Arabis verna）/ 小花屈曲花（Aubrieta parviflora），以及林生葶苈（Draba nemorosa）/ 西班牙葶苈（Draba hispanica）。

研究结果
将9个物种的所有基因归类至基因家族后，我们鉴定出5个基因家族：其在多年生物种lyrata鼠耳芥（Arabidopsis lyrata）和高山山芥（Arabis alpina）中存在注释良好的功能基因，但在所有一年生物种中均未检出。在这5个家族的11个多年生功能基因中，有6个在一年生物种的共线性区域中发现了直系同源假基因或高度分化的基因。本次鉴定出的5个候选家族分别编码：1种激酶、1种氧化还原酶、1种乳酰谷胱甘肽裂解酶、1个F-box蛋白以及1个锌指蛋白。通过比较多年生物种中的活性基因与一年生物种中的假基因或发生显著变异的基因，我们计算了dN与dS值。其中1种激酶的低dN/dS值提示其假基因化事件发生较晚；而其余激酶、F-box蛋白、氧化还原酶及锌指蛋白的假基因化则更接近该一年生-多年生姊妹演化支的分化时间。

研究结论
我们鉴定出5个可能参与了从多年生向一年生生活史转换的基因家族。综合dN/dS分析结果、共线性假基因的存在情况以及基因的潜在功能，F-box家族被认为是未来开展功能研究以确定其是否调控植物生活史的最具潜力的候选靶点。