A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Factors affecting the global distribution of Hydrilla verticillata

Hydrilla verticillata (Hydrocharitaceae) is a submerged freshwater flowering plant within the monotypic genus. Over the geological periods, fossils of this family and genus have shown distinct diversifications between warm and cool fluctuations with more adaptations occurring in warmer periods and suppressions during severely cold paleoclimate changes. Recently, H. verticillata has shown a wide range of adaptive plasticity, allowing successful proliferation into non-native regions, whilst also undergoing unexplained disappearance from its native localities, and this phenomenon has stimulated this inquiry. Against this somewhat complex background, particular interest for this investigation has been focussed on an understanding of which aspects of climate change have contributed towards global adaptations and distribution patterns of H. verticillata. Whilst it is recognised that some of these changes are natural, other aggravating impacts are due to anthropogenic influences. Identifying the appropriate combinations of these climatic factors (temperature, rainfall, photoperiod), in concert with environmental (water level, CO2, salinity, eutrophication), geographical (altitude, latitude) and other factors (UV-B) are necessary precursors for instituting appropriate management strategies. In this respect, control measures are needed in non-native regions and restoration of this plant in native habitats are essential for its ecologically balanced global distribution. © 2021 European Weed Research Societ