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变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目前仍未明确。为鉴定介导一年生与多年生植物性状差异的基因，本研究对十字花科（Brassicaceae）中的四对姐妹群进行了基因含量比较，每对姐妹群均包含一个一年生物种和一个多年生物种，具体为：拟南芥（Arabidopsis thaliana）/ lyrata拟南芥（Arabidopsis lyrata）、蒙布南芥（Arabis montbretiana）/高山南芥（Arabis alpina）、春生南芥（Arabis verna）/小花岩芥（Aubrieta parviflora）以及林地葶苈（Draba nemorosa）/西班牙葶苈（Draba hispanica），此外还额外纳入了一个一年生物种红花荠（Capsella rubella）。
研究结果：将9个物种的全部基因聚类至基因家族后，本研究鉴定出5个基因家族：其中多年生物种lyrata拟南芥与高山南芥中存在注释完整的功能基因，但所有一年生物种中均未检出该类基因。针对上述家族中多年生物种的11个基因，有6个案例可在一年生物种的共线性区域中发现其直系同源假基因或高度分化的同源基因。本次鉴定出的5个候选基因家族分别编码：激酶、氧化还原酶、乳酰谷胱甘肽裂解酶、F-box蛋白以及锌指蛋白。通过对比多年生物种中的功能基因与一年生物种中的假基因或严重分化的同源基因，本研究计算了非同义替换率（dN）与同义替换率（dS）。其中一个激酶家族的低dN/dS值表明其假基因化事件发生较晚；而其余激酶、F-box、氧化还原酶及锌指蛋白家族的假基因化事件则更接近一年生-多年生姐妹群的分化时间。
研究结论：本研究鉴定出5个可能参与从多年生向一年生生活史转变的基因家族。结合dN与dS数据、共线性区域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验证研究以明确其是否调控植物生活史的最具潜力的候选对象。