The Earth BioGenome project: opportunities and challenges for plant genomics and conservation

Abstract

Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115,[4325][4326][4327][4328][4329][4330][4331][4332][4333], which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within-species genetic diversity and the historical aspect of conservation genetics.

CNSA: a data repository for archiving omics data

“…With the development of sequencing technology, the rapid increase of sequencing throughput and the dramatic drop of sequencing cost have made large-scale population genomics research, precision medicine research and biodiversity research possible. For instance, the UK’s 100 000 Genomes Project [ 1 ], the International Cancer Genome Consortium (ICGC) [ 2 ], the Cancer Genome Atlas (TCGA) [ 3 ], the China Kadoorie Biobank (CKB) [ 4 ] and Earth BioGenome Project (EBP) [ 5 ] have been announced or completed in the past decades. However, it poses great challenges in big data deposition, integration and sharing.…”

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

“…The framework of the Transparent Plant tool is an annotated catalog of the tens of thousands of plant genes diversified among all species, a modern‐day expansion of the basic gene function catalog originally envisioned in the Arabidopsis 2010 initiative (Somerville & Dangl, 2000). We support the Earth BioGenome Project (Exposito‐Alonso, Drost, Burbano, & Weigel, 2019), which aims to sequence the genome of many or all extant eukaryotic species, made feasible by new technology and reduced cost. However, sequence information is only the beginning of biological insight: knowledge related to these genes, including their regulation, how they influence metabolism, and how they interact, will need to be acquired.…”

Decoding indigo: the chromosome‐scale genome of Strobilanthes cusia a highly pigmented plant important to diverse ethnic cultures in Asia

“…Not only are the conclusions of this paper immensely informative in their own right, they and the future work proposed by Prof. Liu provide a wonderful example of how next‐generation sequencing combined with biochemistry and deep cultural knowledge can elucidate the genetics underlying the choices made by our forebears. As such, it provides a blueprint that will likely prove of immense use for many aspects of plant biology given the initiation of the Earth Bio‐Genome project (Exposito‐Alonso et al , 2020).…”

“…Indigo is the sole natural blue pigment, and as such has been regarded as highly valuable by textile weavers for several millennia (Balfour‐Paul, 2006). Indeed, ethnobotanical studies have provided evidence that indigo dye was used in clothing in Peru about 6000 years ago (Splitstoser et al , 2016), with its use in India, Egypt, Europe and China all recorded at least 2900 years ago (Xu et al , 2020).…”