A pan-genomic approach to genome databases using maize as a model system

Margaret R Woodhouse,Ethalinda K Cannon,Carson M Andorf,John L Portwood,Mary L Schaeffer,Jack M Gardiner,Lisa C Harper

doi:10.1186/s12870-021-03173-5

Margaret R Woodhouse, Ethalinda K Cannon + Show 5 more

Open Access

https://doi.org/10.1186/s12870-021-03173-5

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Abstract

Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

Highlights

Zea mays ssp. mays is a unique model organism as its broad importance as a food, feed, and fiber product has driven its domestication over thousands of years by the traditional breeding practices of indigenous people [1,2,3], followed by decades of directed breeding since the green revolution and the molecular era [4, 5]
MaizeGDB Pan-Genome: Scripts for the pan-genome and tandem duplicate relationships can be found in the MaizeGDB GitHub repository https://github.com/MaizeGenetics-and-Genomics-Database/Pan-Genome
Using the high-quality Nested Associated Mapping (NAM) founder genomes as a gold standard, we compiled pangene sets accessible through each gene model page, made jumping between genome browsers possible, implemented cross-genome structural variant comparisons, Supplementary Information

Summary

Introduction

Zea mays ssp. mays (maize, corn) is a unique model organism as its broad importance as a food, feed, and fiber product has driven its domestication over thousands of years by the traditional breeding practices of indigenous people [1,2,3], followed by decades of directed breeding since the green revolution and the molecular era [4, 5]. Mays (maize, corn) is a unique model organism as its broad importance as a food, feed, and fiber product has driven its domestication over thousands of years by the traditional breeding practices of indigenous people [1,2,3], followed by decades of directed breeding since the green revolution and the molecular era [4, 5]. Over the last 100 years, research on maize has been instrumental in understanding plant biology, evolution, domestication, development, and genetics [6,7,8,9,10]. Curated maize research data was formally moved into a database in 1991 (MaizeDB) [13].

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