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"Variations"
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Current status of structural variation studies in plants
Summary Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic diversity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever‐greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.
Journal Article
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
Background
Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single algorithm can call every type of SVs with high precision and high recall.
Results
We comprehensively evaluate the performance of 69 existing SV detection algorithms using multiple simulated and real WGS datasets. The results highlight a subset of algorithms that accurately call SVs depending on specific types and size ranges of the SVs and that accurately determine breakpoints, sizes, and genotypes of the SVs. We enumerate potential good algorithms for each SV category, among which GRIDSS, Lumpy, SVseq2, SoftSV, Manta, and Wham are better algorithms in deletion or duplication categories. To improve the accuracy of SV calling, we systematically evaluate the accuracy of overlapping calls between possible combinations of algorithms for every type and size range of SVs. The results demonstrate that both the precision and recall for overlapping calls vary depending on the combinations of specific algorithms rather than the combinations of methods used in the algorithms.
Conclusion
These results suggest that careful selection of the algorithms for each type and size range of SVs is required for accurate calling of SVs. The selection of specific pairs of algorithms for overlapping calls promises to effectively improve the SV detection accuracy.
Journal Article
Copy number evolution and its relationship with patient outcome—an analysis of 178 matched presentation-relapse tumor pairs from the Myeloma XI trial
Structural chromosomal changes including copy number aberrations (CNAs) are a major feature of multiple myeloma (MM), however their evolution in context of modern biological therapy is not well characterized. To investigate acquisition of CNAs and their prognostic relevance in context of first-line therapy, we profiled tumor diagnosis–relapse pairs from 178 NCRI Myeloma XI (ISRCTN49407852) trial patients using digital multiplex ligation-dependent probe amplification. CNA profiles acquired at relapse differed substantially between MM subtypes: hyperdiploid (HRD) tumors evolved predominantly in branching pattern vs. linear pattern in t(4;14) vs. stable pattern in t(11;14). CNA acquisition also differed between subtypes based on
CCND
expression, with a marked enrichment of acquired del(17p) in
CCND2
over
CCND1
tumors. Acquired CNAs were not influenced by high-dose melphalan or lenalidomide maintenance randomization. A branching evolution pattern was significantly associated with inferior overall survival (OS; hazard ratio (HR) 2.61,
P
= 0.0048). As an individual lesion, acquisition of gain(1q) at relapse was associated with shorter OS, independent of other risk markers or time of relapse (HR = 2.00;
P
= 0.021). There is an increasing need for rational therapy sequencing in MM. Our data supports the value of repeat molecular profiling to characterize disease evolution and inform management of MM relapse.
Journal Article
The things that I love about trees
\"[This] picture book ... looks at how a tree changes with the seasons\"--Amazon.com.
Book
The Beijing Climate Center Climate System Model (BCC-CSM): the main progress from CMIP5 to CMIP6
The main advancements of the Beijing Climate Center (BCC) climate system model from phase 5 of the Coupled Model Intercomparison Project (CMIP5) to phase 6 (CMIP6) are presented, in terms of physical parameterizations and model performance. BCC-CSM1.1 and BCC-CSM1.1m are the two models involved in CMIP5, whereas BCC-CSM2-MR, BCC-CSM2-HR, and BCC-ESM1.0 are the three models configured for CMIP6. Historical simulations from 1851 to 2014 from BCC-CSM2-MR (CMIP6) and from 1851 to 2005 from BCC-CSM1.1m (CMIP5) are used for models assessment. The evaluation matrices include the following: (a) the energy budget at top-of-atmosphere; (b) surface air temperature, precipitation, and atmospheric circulation for the global and East Asia regions; (c) the sea surface temperature (SST) in the tropical Pacific; (d) sea-ice extent and thickness and Atlantic Meridional Overturning Circulation (AMOC); and (e) climate variations at different timescales, such as the global warming trend in the 20th century, the stratospheric quasi-biennial oscillation (QBO), the Madden–Julian Oscillation (MJO), and the diurnal cycle of precipitation. Compared with BCC-CSM1.1m, BCC-CSM2-MR shows significant improvements in many aspects including the tropospheric air temperature and circulation at global and regional scales in East Asia and climate variability at different timescales, such as the QBO, the MJO, the diurnal cycle of precipitation, interannual variations of SST in the equatorial Pacific, and the long-term trend of surface air temperature.
Journal Article
A big garden
\"This wonderfully insightful and brilliantly illustrated book on gardens and gardeners will provide hours of absorbing fun while introducing young readers to the joys of planning, planting, and harvesting. In vibrant watercolors Vincent Grave shows us how there's something happening every month in the Big Garden. Renowned landscape designer Gilles Clement's lyrical text gently teaches young readers not only what's involved in planning a garden, but how plants, insects, and humans interact all year long to make the garden thrive. Along the way, we witness a forest of mushrooms, the miracle of eggs, and the incredible universe found in a single flower. In every picture, tiny gardeners busy themselves among the leaves, seeds, and earth. Fascinating, heartfelt, and elegantly produced, this book celebrates the deep connection between humans and nature\"-- Publisher's description.
Book
European Summer Wet-Bulb Temperature: Spatiotemporal Variations and Potential Drivers
Heat stress is projected to intensify with global warming, causing significant socioeconomic impacts and threatening human health. Wet-bulb temperature (WBT), which combines temperature and humidity effects, is a useful indicator for assessing regional and global heat stress variability and trends. However, the variations of European WBT and their underlying mechanisms remain unclear. Using observations and reanalysis datasets, we demonstrate a remarkable warming of summer WBT during the period 1958–2021 over Europe. Specifically, the European summer WBT has increased by over 1.0°C in the past 64 years. We find that the increase in European summer WBT is driven by both near-surface warming temperatures and increasing atmospheric moisture content. We identify four dominant modes of European summer WBT variability and investigate their linkage with the large-scale atmospheric circulation and sea surface temperature anomalies. The first two leading modes of the European WBT variability exhibit prominent interdecadal to long-term variations, mainly driven by a circumglobal wave train and concurrent sea surface temperature variations. The last two leading modes of European WBT variability mainly show interannual variations, indicating a direct and rapid response to large-scale atmospheric dynamics and nearby sea surface temperature variations. Further analysis shows the role of global warming and changes in midlatitude circulations in the variations of summer WBT. Our findings can enhance the understanding of plausible drivers of heat stress in Europe and provide valuable insights for regional decision-makers and climate adaptation planning.
Journal Article