PE0306 Haplotype-Resolved Genome Assemblies and a Pan-Genome of Six Pistachio Cultivars

Trabajo presentado en la International Plant and Animal Genome Conference, celebrada en San Diego, CA (Estados Unidos), del 13 al 18 de enero de 2023Pistachio (Pistacia vera L., 2n =2x = 30) is one of the most economically important long-lived crops, including cashew and mango in the family Anacardiaceae. Although dioecious pistachio trees are xerophytic and highly resilient to abiotic stresses, they require a certain amount of winter rest period to exit bud dormancy and to flower synchronically between male and female trees. The `Kerman¿ (P. vera cv. Kerman) and `Peter¿ (P. vera cv. Peter) have been the dominant pair of female and male cultivars traditionally grown in California for more than 50 years, whereas the understanding of genomic diversity and approaches for pistachio breeding is limited without the reference-quality genome. Genetic diversity, such as structural and gene content variation, is a major source for crop improvement and breeding, which cannot be captured from a single reference genome. In the present study, we report haplotype-resolved chromosome-level reference genomes of six genetically diverse collections of pistachio (`Kerman¿, `Mateur¿, `Sirora¿, Napoletana¿, `Chaparrillo¿, and `T41¿). The diploid assemblies ranged from 568.55 to 608.21 Mb in size with contig N50 of 28 - 37 Mb. More than 98% of conserved orthologs (BUSCO) were represented for all genome assemblies. The dynamics of transposable elements (TEs) were characterized in the genomes where the TEs accounted for about 65 - 68% of the genomes. The gene annotation analyses using Iso-seq data generated from different five tissue types predicted about 38,000 protein-coding genes. Two haplotypes of each genome showed substantial sequence variation, suggesting high heterozygosity in pistachio genomes. Pan-genome construction and analyses characterized remarkable presence-absence gene content variation between cultivars. The reference genomes with fully annotated genes and pan-genome construction serve as rich resources for genomic breeding and improvement and comparative genomics of pistachio

An open-source database for the synthesis of soil radiocarbon data: International Soil Radiocarbon Database (ISRaD) version 1.0

Radiocarbon is a critical constraint on our estimates of the timescales of soil carbon cycling that can aid in identifying mechanisms of carbon stabilization and destabilization and improve the forecast of soil carbon response to management or environmental change. Despite the wealth of soil radiocarbon data that have been reported over the past 75 years, the ability to apply these data to global-scale questions is limited by our capacity to synthesize and compare measurements generated using a variety of methods. Here, we present the International Soil Radiocarbon Database (ISRaD; http://soilradiocarbon.org, last access: 16 December 2019), an open-source archive of soil data that include reported measurements from bulk soils, distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods, samples of soil gas or water collected interstitially from within an intact soil profile, CO2 gas isolated from laboratory soil incubations, and fluxes collected in situ from a soil profile. The core of ISRaD is a relational database structured around individual datasets (entries) and organized hierarchically to report soil radiocarbon data, measured at different physical and temporal scales as well as other soil or environmental properties that may also be measured and may assist with interpretation and context. Anyone may contribute their own data to the database by entering it into the ISRaD template and subjecting it to quality assurance protocols. ISRaD can be accessed through (1) a web-based interface, (2) an R package (ISRaD), or (3) direct access to code and data through the GitHub repository, which hosts both code and data. The design of ISRaD allows for participants to become directly involved in the management, design, and application of ISRaD data. The synthesized dataset is available in two forms: the original data as reported by the authors of the datasets and an enhanced dataset that includes ancillary geospatial data calculated within the ISRaD framework. ISRaD also provides data management tools in the ISRaD-R package that provide a starting point for data analysis; as an open-source project, the broader soil community is invited and encouraged to add data, tools, and ideas for improvement. As a whole, ISRaD provides resources to aid our evaluation of soil dynamics across a range of spatial and temporal scales. The ISRaD v1.0 dataset is archived and freely available at https://doi.org/10.5281/zenodo.2613911 (Lawrence et al., 2019).Max Planck Institute for Biogeochemistry; European Research CouncilEuropean Research Council (ERC) [695101]; USGS Land Change Science mission area; US Department of AgricultureUnited States Department of Agriculture (USDA) [2018-67003-27935]; US Geological Survey Powell Center for the working group on Soil Carbon Storage and FeedbacksOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]