A chromosome-level genome assembly for the desert scorpion Mesobuthus przewalskii from Asian drylands.

Scorpions are an ancient and charismatic group of arthropods with medical importance, but a high-quality reference genome for this group is still lacking. Here we perform whole-genome sequencing of Mesobuthus przewalskii, a desert scorpion endemic to the Taklimakan Desert. We combine PacBio HiFi sequencing and Hi-C chromosome conformation capturing to generate chromosomal-level, haplotype-resolved, and fully annotated genome assembly for this medically important scorpion.

Genomic and Phenotypic Adaptations of Rattus tanezumi to Cold Limit Its Further Northward Expansion and Range Overlap with R. norvegicus.

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins.

OsEIL2 balances rice immune responses against (hemi)biotrophic and necrotrophic pathogens via the salicylic acid and jasmonic acid synergism.

Plants typically activate distinct defense pathways against various pathogens. Heightened resistance to one pathogen often coincides with increased susceptibility to another pathogen. However, the underlying molecular basis of this antagonistic response remains unclear.

Antagonistic control of rice immunity against distinct pathogens by the two transcription modules via salicylic acid and jasmonic acid pathways.

Although the antagonistic effects of host resistance against biotrophic and necrotrophic pathogens have been documented in various plants, the underlying mechanisms are unknown. Here, we investigated the antagonistic resistance mediated by the transcription factor ETHYLENE-INSENSITIVE3-LIKE 3 (OsEIL3) in rice. The Oseil3 mutant confers enhanced resistance to the necrotroph Rhizoctonia solani but greater susceptibility to the hemibiotroph Magnaporthe oryzae and biotroph Xanthomonas oryzae pv.

Phylogeography of the desert scorpion illuminates a route out of Central Asia.

A comprehensive understanding of phylogeography requires the integration of knowledge across different organisms, ecosystems, and geographic regions. However, a critical knowledge gap exists in the arid biota of the vast Asian drylands. To narrow this gap, here we test an "out-of-Central Asia" hypothesis for the desert scorpion by combining Bayesian phylogeographic reconstruction and ecological niche modeling.

The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control.

Many lacewing species (Insecta: Neuroptera) are important predators of pests with great potential in biological control. So far, there is no chromosome-level published genome available for Neuroptera. Here we report a high-quality chromosome-level reference genome for a green lacewing species Chrysopa pallens (Neuroptera: Chrysopidae), which is one of the most important insect natural enemies used in pest biocontrol.

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters.

A novel RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the ongoing outbreak of coronavirus disease 2019 (COVID-19). Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19. However, due to extensive sampling bias and existence of infection clusters during the epidemic spread, direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.

Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean.

Ancestry informative markers play an important role in medical genetics and forensic analyses. Several ancestry informative SNP panels have been developed and validated that can differentiate global populations into continental or major regional groups. These global panels have served as good first-tier genetic markers; however, their performance in discriminating populations within regions appears unsatisfactory.

AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels.

Inferring an individual's ancestry or group membership using a small set of highly informative genetic markers is very useful in forensic and medical genetics. However, given the huge amount of SNP data available from a diverse of populations, it is challenging to develop informative panels by exhaustively searching for all possible SNP combinations. In this study, we formulate it as an algorithm problem of selecting an optimal set of SNPs that maximizes the inference accuracy while minimizes the set size.

[Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis].

The next generation sequencing (NGS) technology has been playing important roles in genetic diagnosis of diseases in recent years, and serving as a technological basis of precision medicine. In analyzing NGS data, the variant annotation is an important step. In this study, we developed a computationally efficient software (BIG-Annotator) to perform functional annotation for whole-genome single nucleotide polymorphisms.

Inferring Chinese surnames with Y-STR profiles.

Co-ancestry of human surnames and Y-chromosomes in most human populations and social groups suggests the possibility of inferring one from the other. However, such an intuitive perspective remains to be formally explored. In the present study, we develop two computational methods, based on cosine distance (d) and coalescence distance (d) respectively, to infer surnames from Y-STR profiles.

Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons.

The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons.

Impact of climate changes from Middle Miocene onwards on evolutionary diversification in Eurasia: insights from the mesobuthid scorpions.

The aridification from Middle Miocene onwards has transformed the Asian interior into an arid environment, and the Pleistocene glacial-interglacial oscillations exerted further ecological impact. Therefore, both aridification and glaciation would have considerably influenced the evolution of many mid-latitude species in temperate Asia. Here, we tested this perspective by a phylogeographic study of the mesobuthid scorpions across temperate Asia using one mitochondrial and three nuclear genes.

Eight polymorphic microsatellite markers developed in the Chinese scorpion, Mesobuthus martensii (Scorpiones: Buthidae).

Eight polymorphic di- and trinucleotide microsatellite loci were developed in the Chinese scorpion, Mesobuthus martensii. The expected heterozygosity at these loci ranges from 0.019 to 0.