Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis

Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type—which included inversions, duplications, deletions, translocations, and mobile element insertions—was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.Peer reviewe

Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low-copy loci

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18 555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (maximum parsimony, maximum likelihood, and Bayesian inference) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian, and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in the North Pacific region in late early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since mid-Miocene. The late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America, and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, central Asia, and western North America converged to form the beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which could shed new insights into the formation of the temperate biome in the Northern Hemisphere.This work was supported by the National Natural Science Foundation of China (Grant Nos. 31770236, 30760016, and 31560064) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000).1 Introduction 2 Material and Methods 2.1 Taxon sampling 2.2 Screening of nuclear single/low-copy orthologous locus 2.3 DNA extraction, PCR protocol, and sequencing 2.4 Phylogenetic analyses and molecular dating 2.5 Ancestral area reconstruction 3 Results 3.1 Concatenated tree 3.2 Species tree and molecular dating 3.3 Ancestral area reconstruction 4 Discussion 4.1 Nearly resolved and well supported phylogeny of Fagus 4.2 Species delimitation of three segregates within Fagus 4.3 Biogeographic history of beech species Acknowledgement

NTIRE 2023 Quality Assessment of Video Enhancement Challenge

This paper reports on the NTIRE 2023 Quality Assessment of Video Enhancement Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2023. This challenge is to address a major challenge in the field of video processing, namely, video quality assessment (VQA) for enhanced videos. The challenge uses the VQA Dataset for Perceptual Video Enhancement (VDPVE), which has a total of 1211 enhanced videos, including 600 videos with color, brightness, and contrast enhancements, 310 videos with deblurring, and 301 deshaked videos. The challenge has a total of 167 registered participants. 61 participating teams submitted their prediction results during the development phase, with a total of 3168 submissions. A total of 176 submissions were submitted by 37 participating teams during the final testing phase. Finally, 19 participating teams submitted their models and fact sheets, and detailed the methods they used. Some methods have achieved better results than baseline methods, and the winning methods have demonstrated superior prediction performance

Reexaminations of the effects of magnetic field on the nucleation of undercooled Cu melt

International audienc

Strong magnetic field effect on the nucleation of a highly undercooled Co-Sn melt

International audienc

Overheating dependent undercooling in a hypoeutectic Co–B alloy

International audienc

Experimental platform for solidification and in-situ magnetization measurement of undercooled melt under strong magnetic field

International audienc

Subtle East–West Phylogeographic Break of <i>Asteropyrum</i> (Ranunculaceae) in Subtropical China and Adjacent Areas

East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China