Buitrago-Flórez Francisco Javier, Restrepo Silvia, Riaño-Pachón Diego Mauricio
Group of Computational and Evolutionary Biology, Universidad de los Andes, Bogotá, Colombia; Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia.
Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia.
PLoS One. 2014 Nov 6;9(11):e111841. doi: 10.1371/journal.pone.0111841. eCollection 2014.
The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.
不等鞭毛类生物的生物多样性十分显著；它们涵盖了从大型多细胞海藻到微小单细胞物种的范围，包含许多在生态上具有重要意义的自养生物（如硅藻、褐藻）以及异养生物（如卵菌）群体。转录因子（TFs）和其他转录调节因子（TRs）调控基因表达的时空特性。大量的转录调节蛋白已被鉴定，并根据序列相似性分为不同家族。这项工作的目的是确定不等鞭毛类不同物种中的TF和TR组成，以便了解这些调节因子如何促成它们所表现出的多样性。我们在11种不等鞭毛类物种中鉴定并分类了63个TF和TR家族。在一些物种中，我们发现了具有高度相对重要性的基因家族。考虑到所鉴定的63个TF和TR家族，确定有28个TF和TR家族与特定性状呈正相关，如预测蛋白的数量、鞭毛数量以及生命周期中的细胞类型数量。此外，我们发现了一些特定物种和进化枝特有的TF和TR家族的增减情况，以及自养物种特有的两个高丰度家族和异养物种特有的三个高丰度家族。首次对不等鞭毛类中的TF和TR家族进行了系统搜索。鉴于存在几种重要的动植物病原体以及参与碳循环的重要物种，揭示这些家族之间的关系以及该类群复杂性的尝试可能具有重大影响。在这项工作中鉴定出的特定TF和TR家族似乎与不等鞭毛类群中的特定性状相关，并且可能与不等鞭毛类的高度复杂性和多样性相关。
