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Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication–informed collinear anchor identification between genomes and performs base pair–resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor–binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation. ; This project is supported by the United States Department of Agriculture Agricultural Research Service, NSF No. 1822330, NSF No. 1854828, the European Union's Horizon 2020 Framework Programme under the DeepHealth project [825111], the European Union Regional Development Fund within the framework of The European Regional Development Fund Operational Program of Catalonia 2014 to 2020 with a grant of 50% of total cost eligible under the DRAC project [001-P-001723], and National Natural Science Foundation of China No. 31900486. M.C.S. was supported by NSF Postdoctoral Research Fellowship in Biology No. 1907343. M.M. was partially supported by the Spanish Ministry of Economy, Industry, and Competitiveness under Ramón y Cajal (RYC) fellowship number RYC-2016-21104. ; Peer Reviewed ; Postprint (published version)

This open access book is the result of an expert panel convened by the Cornell Atkinson Center for Sustainability and Nature Sustainability. The panel tackled the seventeen UN Sustainable Development Goals (SDGs) for 2030 head-on, with respect to the global systems that produce and distribute food. The panel's rigorous synthesis and analysis of existing research leads compellingly to multiple actionable recommendations that, if adopted, would simultaneously lead to healthy and nutritious diets, equitable and inclusive value chains, resilience to shocks and stressors, and climate and environmental sustainability.

Technological and institutional innovations in agri-food systems (AFSs) over the past century have brought dramatic advances in human well-being worldwide. Yet these gains increasingly appear unsustainable due to massive, adverse spillover effects on climate, natural environment, public health and nutrition, and social justice. How can humanity innovate further to bring about AFS transformations that can sustain and expand past progress, while making them healthier for all people and for the planet that must sustain current and future generations? This report was commissioned by the Cornell Atkinson Center for Sustainability in response to an invitation from the journal Nature Sustainability, which—in collaboration with its new sister journal, Nature Food—wanted to devote its 2020 expert panel to this topic. The panel brought together experts who come from many different continents and who span a wide range of disciplines and organizations—from industry and universities to social movements, governments, philanthropies, institutional and venture capital investors, and multilateral agencies. The panel synthesized the best current science to describe the present state of the world's AFSs and key external drivers of AFS changes over the next 25–50 years, as well as tease out key lessons from the COVID-19 pandemic experience this year. As is increasingly widely recognized, the costs that farmers and downstream value chain actors incur and the prices consumers pay understate foods' true costs to society once one accounts for adverse environmental, health, and social spillover effects. Inevitable demographic, economic, and climate change in the coming decades will catastrophically aggravate these problems under business-as-usual scenarios. Innovations will be needed to facilitate concerted, coordinated efforts to transition to more healthy, equitable, resilient, and sustainable AFSs.