High-throughput sequencing data and the impact of plant gene annotation quality

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http://hdl.handle.net/10138/300421

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Vaattovaara , A F M , Leppälä , J M , Salojärvi , J T & Wrzaczek , M A 2019 , ' High-throughput sequencing data and the impact of plant gene annotation quality ' , Journal of Experimental Botany , vol. 70 , no. 4 , ery43 , pp. 1069-1076 . https://doi.org/10.1093/jxb/ery434

Title: High-throughput sequencing data and the impact of plant gene annotation quality
Author: Vaattovaara, Aleksia Fanni Maria; Leppälä, Johanna Maria; Salojärvi, Jarkko Tapani; Wrzaczek, Michael Alois
Contributor organization: Organismal and Evolutionary Biology Research Programme
Viikki Plant Science Centre (ViPS)
Bioinformatics for Molecular Biology and Genomics (BMBG)
Receptor-Ligand Signaling Group
Plant Biology
Date: 2019-02-01
Language: eng
Number of pages: 8
Belongs to series: Journal of Experimental Botany
ISSN: 0022-0957
DOI: https://doi.org/10.1093/jxb/ery434
URI: http://hdl.handle.net/10138/300421
Abstract: The use of draft genomes of different species and re-sequencing of accessions and populations are now a common tool for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits including plant stress tolerance or development. In both cases high quality gene annotation, the identification of protein-coding regions, gene promoters and 5’ and 3’ untranslated regions, is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families and segmentally duplicated genes. In this opinion paper we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies and the identification of orthologous genes in plants. Furthermore, we predict that incorporating the accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
Subject: ARABIDOPSIS-THALIANA
CORE GENES
DISCOVERY
DIVERSITY
DUPLICATION
EVOLUTION
GENOME-WIDE ASSOCIATION
GWAS
Gene families
PHENOTYPES
PIPELINE
TRANSPOSABLE ELEMENTS
genome annotation
high-throughput sequencing
phylogeny
translational research
1183 Plant biology, microbiology, virology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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