Тип публикации: статья из журнала

Год издания: 2022

Идентификатор DOI: 10.3390/ijms23031735

Ключевые слова: conifer, gymnosperms, promoter prediction, tata-box, transcription factor binding site, transcription start site

Аннотация: The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), Показать полностьюexperimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Журнал: International Journal of Molecular Sciences

Выпуск журнала: Vol. 23, Is. 3

Номера страниц: 1735

ISSN журнала: 16616596

Издатель: MDPI

• Bondar E.I. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center” Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation)
• Troukhan M.E. (Persephone Software LLC, Agoura Hills, CA 91301, United States)
• Tatarinova T.V. (Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation, Department of Biology, University of La Verne, La Verne, CA 91750, United States, Functional Genomics Group, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russian Federation, A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russian Federation)
• Krutovsky K.V. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, 37077, Germany, Center for Integrated Breeding Research, Georg-August University of Göttingen, Göttingen, 37075, Germany, Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russian Federation, Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, 394087, Russian Federation, Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation)

• Scopus
• Web of Science Core Collection