Asma Hasiba, Halfon Marc S
Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
Insects. 2021 Jun 29;12(7):591. doi: 10.3390/insects12070591.
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.
在整个进化谱系中，越来越多的昆虫基因组正在被测序。不仅对基因进行全面注释，而且对调控区域进行全面注释，对于充分利用这种测序的全部益处至关重要。在测序技术以及经验性和计算性发现策略的发展推动下，过去几十年见证了我们在识别调控模块（CRM）方面的巨大进展，调控模块是指如增强子等在调节转录中起主要作用的序列。然而，为新测序的昆虫基因组提供及时且全面的调控注释仍是一项持续的挑战。我们在此回顾用于识别模式昆虫和非模式昆虫物种中CRM的方法，并重点介绍我们开发的两种工具，REDfly和SCRMshaw。这些资源可以以强大的组合方式配对，以促进对广泛物种的昆虫调控注释，其准确性等于或优于其他最先进的方法。
