Genome-wide Prediction of Transcription Start Site in Four Conifer Species

Poster (download)

104

Eugeniia I. Bondar¹, Dmitry A. Kuzmin², Konstantin V. Krutovsky³, Vadim V. Sharov⁴, Tatiana V. Tatarinova⁵
¹Laboratory of Forest Genomics, Siberian Federal University; Laboratory of Genomeic Research and Biotechnology, FRC KSC SB RAS, Krasnoyarsk, Russia, bondar.ev@ksc.krasn.ru
²Laboratory of Forest Genomics Siberian Federal University; Department of High Performance Computing, Siberian Federal University, Krasnoyarsk, Russia, dm.kuzmin@gmail.com
³Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk, Russia; Department of Forest Genetics and Forest Tree Breeding, Georg-August of GГ¶ttingen, GГ¶ttingen, Germany; Laboratory of Population Genetics, Vavilov Institute of General Genetics, Moscow, Russia; Department of Ecosystem Science and Management Texas A&M University College Station, TX, USA, konstantin.krutovsky@forst.uni-goettingen.de
⁴Laboratory of Genomeic Research and Biotechnology, FRC KSC SB RAS; Laboratory of Forest Genomics, Siberian Federal University; Department of High Performance Computing, Siberian Federal University, Krasnoyarsk, Russia, sharvadim07@ya.ru
⁵Department of Biology, University of La Verne, La Verne, USA; Functional Genomics Group, Vavilov Institute for General Genetics, Moscow, Russia; Siberian Federal University, Krasnoyarsk, Russia; Bioinformatics Center of IITP RAS, Moscow, Russia, ttatarinova@laverne.edu

Current draft annotations for sequenced conifer genomes are preliminary and limited, but provide opportunities for further structural and functional analysis. We attempted to improve the existing genome annotations by marking 5вЂ™-UTRs in the four conifer species Pinus taeda, Picea glauca, Picea abies and Larix sibirica. Prediction of transcription start sites (TSS) was performed on the promoter sequences of genes with RNA or protein support using TSS prediction program TSSPlant. The distribution of 5вЂ™-UTR lengths from the annotations of several model plants was used to select the best prediction per gene. Frequency of TATA(A/T)A(A/T) motif in the predicted TSS-centered promoter regions showed a pronounced peak around 60 bp upstream of TSS.

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Elena Zemlyanskaya

4 years ago

Thank you very much for an interesting presentation!
You described the use of RNA-seq data for verification of the existing gene models. Did you considered RNA-seq data for TSS prediction as well?

Eugeniia Bondar

Reply to Elena Zemlyanskaya

Hello, Elena. RNA-seq data is commonly used for building gene models and verifying gene and exon coordinates during annotation. Although it is not mentioned in the poster, we made a comparison between 5′-UTRs predicted by RNA-seq data during the annotation and 5′-UTRs predicted by TSSPlant method. But we did not use RNA in the TSS prediction process.