Perennial Staple Crops: Yields, Distribution, and Nutrition in the Global Food System

Staple crops, which have large amounts of carbohydrates, proteins, and/or fats, provide the bulk of calories in people's diets. Perennial plants, which can be productive for many years without the need for replanting, can produce staple foods and environmental benefits, but their agronomic and nutritional properties haven't been considered synthetically in comparison to annual staples. Here we offer a framework to classify perennial staple crops according to their nutritional categories and cultivation status. We assemble literature to report on the yield potential of 51 perennial staple crops, only 15 of which are well-characterized in existing global datasets. We show the extent and distribution of perennial staple crop production in relation to annual crop types, calculate the carbon stocks they hold, and analyze their nutritional content for three macronutrients and nine micronutrients. We found that most perennial staple crops are regional crops (not globally traded) that grow in the subtropics to tropics. At least one perennial staple crop in each of the five nutritional categories has yields over 2.5 t/ha, in some cases considerably higher, competitive with and in many cases exceeding those of nutritionally comparable annual staples. Perennial staple crops only comprise ~4.5% of total cropland. They hold a modest ~11.4 GtC above and below ground, less than one third of the anthropogenic carbon-equivalent emissions for the year 2018, but more than the ~9 GtC held by the same amount of annual cropland. If linear growth in land under perennial staple production continues to 2040, and replaces only annual cropland, an additional ~0.95 GtC could be sequestered. Many perennial crops also had competitive macronutrient density and yield (per unit area) compared to annual staples; moreover, specific perennial staples are abundant in specific micronutrients, indicating that they can be a nutrient-dense part of diets, unlike the most ubiquitous annual staple crops (corn, wheat, rice) that do not appear in the top 85th percentile for any of the nine micronutrients analyzed. Transition of land and diets to perennial staple crops, if judiciously managed, can provide win-win solutions for both food production and ecosystems.

Evosystem Services: Rapid Evolution and the Provision of Ecosystem Services

Evolution is recognized as the source of all organisms, and hence many ecosystem services. However, the role that contemporary evolution might play in maintaining and enhancing specific ecosystem services has largely been overlooked. Recent advances at the interface of ecology and evolution have demonstrated how contemporary evolution can shape ecological communities and ecosystem functions. We propose a definition and quantitative criteria to study how rapid evolution affects ecosystem services (here termed contemporary evosystem services) and present plausible scenarios where such services might exist. We advocate for the direct measurement of contemporary evosystem services to improve understanding of how changing environments will alter resource availability and human well-being, and highlight the potential utility of managing rapid evolution for future ecosystem services.

Kleat: cleavage site analysis of transcriptomes

In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq data, as the latter are already widely applied to identify other relevant information, such as mutations, alternative splicing and chimeric transcripts. Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3' UTRs. We demonstrate the performance of KLEAT on three cell line RNA-seq libraries constructed and sequenced by the ENCODE project, and assembled using Trans-ABySS. Validating the KLEAT predictions with matched ENCODE RNA-seq and RNA-PET libraries, we show that the tool has over 90% positive predictive value when there are at least three RNA-seq reads supporting a poly(A) tail and requiring at least three RNA-PET reads mapping within 100 nucleotides as validation. We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3' UTR ends, and show that it performs favourably, based on an ROC-like curve.

JAGuaR: junction alignments to genome for RNA-seq reads

JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. Reads aligned to the transcript models are then re-mapped on to genomic coordinates, transforming alignments that span multiple exons into large-gapped alignments on the genome. While JAGuaR does not detect novel junctions, we demonstrate how JAGuaR generates fast and accurate transcriptome alignments, which allows for both sensitive and specific SNV calling.