Parisot Nicolas, Ribeiro Lopes Mélanie, Peignier Sergio, Baa-Puyoulet Patrice, Charles Hubert, Calevro Federica, Callaerts Patrick
INSA Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France.
INSA Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France.
Insect Biochem Mol Biol. 2025 Feb;177:104217. doi: 10.1016/j.ibmb.2024.104217. Epub 2024 Nov 22.
The pea aphid, Acyrthosiphon pisum, is an emerging model system in functional and comparative genomics, in part due to the availability of new genomic approaches and the different sequencing and annotation efforts that the community has dedicated to this important crop pest insect. The pea aphid is also used as a model to study fascinating biological traits of aphids, such as their extensive polyphenisms, their bacteriocyte-confined nutritional symbiosis, or their adaptation to the highly unbalanced diet represented by phloem sap. To get insights into the molecular basis of all these processes, it is important to have an appropriate annotation of transcription factors (TFs), which would enable the reconstruction/inference of gene regulatory networks in aphids. Using the latest version of the A. pisum genome assembly and annotation, which represents the first chromosome-level pea aphid genome, we annotated the complete repertoire of A. pisum TFs and complemented this information by annotating genes encoding chromatin-associated and basal transcription machinery proteins. These annotations were done combining information from the model Drosophila melanogaster, for which we also provide a revisited list of these proteins, and de novo prediction. The comparison between the two model systems allowed the identification of major losses or expansions in each genome, while a deeper analysis was made of ZNF TFs (with certain families expanded in the pea aphid), and the Hox gene cluster (showing reorganization in gene position in the pea aphid compared to D. melanogaster). All annotations are available to the community through the Aphid Transcription Factors database (ATFdb), consolidating the various annotations we generated. ATFdb serves as a valuable resource for gene regulation studies in aphids.
豌豆蚜（Acyrthosiphon pisum）是功能基因组学和比较基因组学中一个新兴的模式系统，部分原因是新的基因组学方法的出现，以及科学界为这种重要的农作物害虫投入了不同的测序和注释工作。豌豆蚜还被用作研究蚜虫迷人生物学特性的模型，比如它们广泛的多型现象、局限于含菌细胞的营养共生关系，或者它们对以韧皮部汁液为代表的高度不均衡饮食的适应。为了深入了解所有这些过程的分子基础，对转录因子（TFs）进行适当的注释很重要，这将有助于重建/推断蚜虫的基因调控网络。利用豌豆蚜基因组组装和注释的最新版本（这是首个染色体水平的豌豆蚜基因组），我们注释了豌豆蚜TFs的完整目录，并通过注释编码与染色质相关的蛋白质和基础转录机制蛋白质的基因来补充这些信息。这些注释结合了模式生物黑腹果蝇的信息（我们也提供了该物种这些蛋白质的修订列表）以及从头预测。对这两个模式系统的比较有助于识别每个基因组中的主要缺失或扩增情况，同时对锌指TFs（某些家族在豌豆蚜中有所扩增）和Hox基因簇（与黑腹果蝇相比，豌豆蚜的基因位置发生了重组）进行了更深入的分析。所有注释通过蚜虫转录因子数据库（ATFdb）向科学界公开，整合了我们生成的各种注释。ATFdb是蚜虫基因调控研究的宝贵资源。
