Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes.

ABSTRACT:

Premise

Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions.

Methods

The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The

SUBMITTER: Vuruputoor VS 

PROVIDER: S-EPMC10439824 | biostudies-literature | 2023 Jul-Aug

REPOSITORIES: biostudies-literature