Gene space completeness in complex plant genomes

Current Opinion in Plant Biology
Michiel Van BelKlaas Vandepoele

Abstract

Genome annotations offer ample opportunities to study gene functions, biochemical and regulatory pathways, or quantitative trait loci in plants. Determining the quality and completeness of a genome annotation, and maintaining the balance between them, are major challenges, even for genomes of well-studied model organisms. In this review, we present a historical overview of the complexity in different plant genomes and discuss the hurdles and possible solutions in obtaining a complete and high-quality genome annotation. We illustrate there is no clear-cut answer to solve these challenges for different gene types, but provide tips on guiding the iterative process of generating a superior genome annotation, which is a moving target as our knowledge about plant genomics increases and additional data sources become available.

Citations

Dec 12, 2019·The Plant Journal : for Cell and Molecular Biology·Alexander J Trouern-TrendJill L Wegrzyn
May 10, 2020·Nature Communications·Shujun OuDoreen Ware
Aug 9, 2020·Frontiers in Plant Science·Mohammad PourkheirandishMohan B Singh
Sep 4, 2020·Proceedings of the National Academy of Sciences of the United States of America·Peter A CrispNathan M Springer
Jul 2, 2021·Nucleic Acids Research·François BucchiniKlaas Vandepoele
Sep 26, 2021·The Plant Genome·Bruno Contreras-MoreiraPaul Flicek
Nov 9, 2021·Nucleic Acids Research·Michiel Van BelKlaas Vandepoele

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