The landscape of plant genomics after 20 years

Abstract Background The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. Although the ELIXIR Core Data Resources and other established infrastructures provide comprehensive and long-term stable services and platforms for FAIR data management, a large quantity of research data is still hidden or at risk of getting lost. Currently, high-throughput plant genomics and phenomics technologies are producing research data in abundance, the storage of which is not covered by established core databases. This concerns the data volume, e.g., time series of images or high-resolution hyper-spectral data; the quality of data formatting and annotation, e.g., with regard to structure and annotation specifications of core databases; uncovered data domains; or organizational constraints prohibiting primary data storage outside institional boundaries. Results To share these potentially dark data in a FAIR way and master these challenges the ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) implements a “bring the infrastructure to the data” approach, which allows research data to be kept in place and wrapped in a FAIR-aware software infrastructure. This article presents new features of the e!DAL infrastructure software and the PGP repository as a best practice on how to easily set up FAIR-compliant and intuitive research data services. Furthermore, the integration of the ELIXIR Authentication and Authorization Infrastructure (AAI) and data discovery services are introduced as means to lower technical barriers and to increase the visibility of research data. Conclusion The e!DAL software matured to a powerful and FAIR-compliant infrastructure, while keeping the focus on flexible setup and integration into existing infrastructures and into the daily research process.

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Advances in Cereal Crop Genomics for Resilience under Climate Change

Life ◽

10.3390/life11060502 ◽

2021 ◽

Vol 11 (6) ◽

pp. 502

Author(s):

Tinashe Zenda ◽

Songtao Liu ◽

Anyi Dong ◽

Huijun Duan

Keyword(s):

Climate Change ◽

Genome Sequencing ◽

Gene Editing ◽

Agronomic Traits ◽

Cereal Crops ◽

Agricultural System ◽

Plant Genomics ◽

Crop Species ◽

Underutilized Species ◽

Recent Developments

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

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Comparative Plant Genomics. Frontiers and Prospects

PLANT PHYSIOLOGY ◽

10.1104/pp.104.900148 ◽

2005 ◽

Vol 138 (2) ◽

pp. 545-547 ◽

Cited By ~ 18

Author(s):

Ana L. Caicedo ◽

Michael D. Purugganan

Keyword(s):

Plant Genomics

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LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

10.1101/2021.01.25.428044 ◽

2021 ◽

Author(s):

Patrick Driguez ◽

Salim Bougouffa ◽

Karen Carty ◽

Alexander Putra ◽

Kamel Jabbari ◽

...

Keyword(s):

De Novo ◽

Rapid Development ◽

Plant Genome ◽

Plant Genomics ◽

High Quality ◽

High Molecular Weight Dna ◽

Tissue Samples ◽

Sequencing Technologies ◽

The Cost ◽

New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

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