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. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.

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. Here, we demonstrate that mutants defective in the transcription factor ETHYLENE-INSENSITIVE 3-LIKE 2 (OsEIL2) exhibited enhanced resistance to the biotrophic bacterial pathogen Xanthomonas oryzae pv oryzae and to the hemibiotrophic fungal pathogen Magnaporthe oryzae, but enhanced susceptibility to the necrotrophic fungal pathogen Rhizoctonia solani. Furthermore, necrotroph-induced OsEIL2 binds to the promoter of OsWRKY67 with high affinity, leading to the upregulation of salicylic acid (SA)/jasmonic acid (JA) pathway genes and increased SA/JA levels, ultimately resulting in enhanced resistance. However, biotroph- and hemibiotroph-induced OsEIL2 targets OsERF083, resulting in the inhibition of SA/JA pathway genes and decreased SA/JA levels, ultimately leading to reduced resistance. Our findings unveil a previously uncharacterized defense mechanism wherein two distinct transcriptional regulatory modules differentially mediate immunity against pathogens with different lifestyles through the transcriptional reprogramming of phytohormone pathway genes.

First report of Calonectria canadiana causing peach fruit rot in China.

Peach (Prunus persica (L.) Batsch) is one of the most popular fruits grown in Northern China. In July 2021, a fruit rot outbreak on the peach cultivar "Yonglian Sweet" occurred after unusual rains in Baoding, Hebei Province, China. Sixty peach trees from three orchards were assessed, and a 30% disease incidence was estimated. The disease initiated as a small concave spot on the fruit surface expanding circularly rotting the fruit (3-5 cm deep) with the appearance of grayish-white mycelia (Figure S1A). The infected fruit did not disintegrate but turned light brown. To identify the pathogen, 20 infected fruits were collected, and fruit tissues from lesion margins were inoculated on the potato dextrose agar (PDA) medium. A total of 15 fungal pure cultures with highly similar morphological characteristics were obtained by the hyphal-tipping method. The fungal culture formed smooth-edged colonies of extensive, dense, wooly aerial mycelium, with color changing from sienna to luteous, and to grayish-white along the radius of colonies (Figure S1B) Chlamydospores were extensive and developed micro-sclerotia after 20 d of growth. The conidiophore produced three branches in a "broom" shape, with the primary branch ranging 7.5-25.0 µm in length, the secondary branch 5.5-15.5 µm, and the tertiary branch 10-12.5 µm (N = 30). The top of the tertiary branch tapered and produced conidia. Conidia were colorless and culm-like, 40.0-57.5 µm long and 3.8-6.25 µm wide (N = 30). Hyphae occasionally produced spherical chlamydospores with a diameter of around 7.5 µm (N = 30). Conidia germinated after 12 h in moist conditions, and germ tubes originated from multiple points on the conidia. Based on these morphological features, the isolated fungus was identified as Calonectria spp. (Lombard et al. 2010). Six loci, including ITS, act, cmdA, his3, tef1, and tub2, were amplified and sequenced for molecular identification of an isolate F099 using primers listed in Table S1. The obtained ITS (528 bp, GenBank accession no. OL635556), act (263 bp, OL694221), cmdA (470 bp, OL694222), his3 (432 bp, OL694223), tef1 (487 bp, OL694224), and tub2 (535 bp, OL694225) sequences showed 100% similarity to the ex-type strain of Calonectria canadiana, CMW 23673 (accession nos. MT359667, MT334976, MT335206, MT335446, MT412737, and MT412958, respectively; Figure S1D) (Kang et al. 2001, Lechat et al. 2010, Liu et al. 2020). The isolate F099 of C. canadiana was further subjected to pathogenicity tests. Koch's postulates were performed by placing three mycelial disks (ten-day old, 5 mm) with conidia on the sterile needle-acupunctured surface of healthy fruits of the peach cultivar "Yonglian Sweet" (N= 10). Mock inoculations with sterile PDA disks were served as a control. All the inoculated fruits were kept in a moist chamber (25℃, 16-h light and 8-h dark period). The inoculation assay was repeated twice. Rotting symptoms developed on all the inoculated fruits about 5 days post-inoculation (dpi) and grayish-white mycelia appeared around ten days post inoculation while mock inoculated fruits did not show any rotting. The pathogen of interest was re-isolated from the inoculated fruits and validated as C. canadiana by ITS and tef1 sequences. All above evidence collectively indicates that the fungal pathogen causing the peach fruit rot is C. canadiana. The new host plant and new geographic distribution reported here will inform future management of this fungal species.

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. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species tree even in presence of excessive incomplete lineage sorting. Concatenation, mp-est and SVDQuartets were unreliable when the species tree contains very short internal branches. Likelihood ratio test of gene flow suggests a small amount of migration from Hylobates moloch to H. pileatus, while cross-genera migration is absent or rare. Our results highlight the utility of coalescent-based methods in addressing challenging species tree problems characterized by short internal branches and rampant gene tree-species tree discordance.

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. To boost ancestry inference for regional populations, second-tier panels with more refined discrimination power among subpopulations within each of the regions need to be developed. In East Asia, Han Chinese, Japanese, and Korean show highly similar externally visible characteristics and are genetically closely related. Reliable ancestry informative genetic markers appear invaluable in discriminating these populations. In the present study, we compiled a genome-wide SNP dataset composing of 317,439 clean SNPs for a total of 1101 unrelated individuals from Han Chinese (817), Koreans (184), and Japanese (100). From this starting dataset, we developed a set of four nested ancestry informative SNP panels including 36, 59, 98, and 142 SNPs, respectively. The results of cross-validation tests indicate that these panels can discriminate the Chinese Han, Japanese, and Korean populations with overall average accuracies ranging from 90% to 99%. In the further performance assessments, these panels also manifested high sensitivity and specificity. In combination with the first-tier global panels, these second-tier panels would contribute to medical genetics and forensic research in East Asia.

[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. BIG-Annotator integrates the widely used databases and pipelines for variant annotation of genetic diseases and tumors, and follows the 2015 ACMG-AMP Standard Guide for Interpretation and Reporting of Clinical Variants. BIG-Annotator is ten times faster than the existing software, and suitable for annotating genomic sequencing data from large samples. Here we present two analysis cases of genetic diagnosis using BIG-Annotator to show its applications.

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. oryzae. OsEIL3 directly activates OsERF040 transcription while repressing OsWRKY28 transcription. The infection of R. solani and M. oryzae or Xoo influences the extent of binding of OsEIL3 to OsWRKY28 and OsERF040 promoters, resulting in the repression or activation of both salicylic acid (SA)- and jasmonic acid (JA)-dependent pathways and enhanced susceptibility or resistance, respectively. These results demonstrate that the distinct effects of plant immunity to different pathogen types are determined by two transcription factor modules that control transcriptional reprogramming and the SA and JA pathways.

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. Concordant mitochondrial and nuclear gene trees were obtained, which are consistent with species tree inferred using a Bayesian approach. The age of the most recent common ancestor (MRCA) of all the studied scorpions was estimated to be 12.49 Ma (late Middle Miocene); Mesobuthus eupeus diverged from the clade composing Mesobuthus caucasicus and Mesobuthus martensii in early Late Miocene (10.21 Ma); M. martensii diverged from M. caucasicus at 5.53 Ma in Late Miocene. The estimated MRCA ages of M. martensii and the Chinese lineage of M. eupeus were 2.37 and 0.68 Ma, respectively. Central Asia was identified as the ancestral area for the lineage leading to M. martensii and M. caucasicus and the Chinese lineage of M. eupeus. The ancestral habitat of the genus Mesobuthus is likely to have been characterized by an arid environment; a shift towards more humid habitat occurred in the MRCA of M. martensii and a lineage of M. caucasicus, finally leading to the adaptation of M. martensii to humid environment. Our data strongly support the idea that the stepwise intensified aridifications from Mid-Miocene onwards drove the diversification of mesobuthid scorpions, and suggest that M. martensii and M. eupeus observed today in China originated from an ancestral lineage distributed in Central Asia. Both the colonization and the ensuing evolution of these species in East Asia appear to have been further moulded by Quaternary glaciations.

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 Mesobuthus mongolicus by combining Bayesian phylogeographic reconstruction and ecological niche modeling. Phylogenetic analyses of one mitochondrial and three nuclear loci and molecular dating revealed that M. mongolicus represents a coherent lineage that diverged from its most closely related lineage in Central Asia about 1.36 Ma and underwent radiation ever since. Bayesian phylogeographic reconstruction indicated that the ancestral population dispersed from Central Asia gradually eastward to the Gobi region via the Junggar Basin, suggesting that the Junggar Basin has severed as a corridor for Quaternary faunal exchange between Central Asia and East Asia. Two major dispersal events occurred probably during interglacial periods (around 0.8 and 0.4 Ma, respectively) when climatic conditions were analogous to present-day status, under which the scorpion achieved its maximum distributional range. M. mongolicus underwent demographic expansion during the Last Glacial Maximum, although the predicted distributional areas were smaller than those at present and during the Last Interglacial. Development of desert ecosystems in northwest China incurred by intensified aridification might have opened up empty habitats that sustained population expansion. Our results extend the spatiotemporal dimensions of trans-Eurasia faunal exchange and suggest that species' adaptation is an important determinant of their phylogeographic and demographic responses to climate changes.

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. The genome was sequenced using a combination of PacBio and Hi-C technologies and assembled into seven chromosomes with a total size of 517.21 Mb, occupying 96.07% of the genome sequence. A total of 12,840 protein-coding genes were identified and approximately 206.21 Mb of repeated sequences were annotated. Phylogenetic analyses indicated that C. pallens diverged from its common ancestor with Tribolium castaneum (Coleoptera) approximately 300 million years ago. The gene families involved in digestion, detoxification, chemoreception, carbohydrate metabolism, immunity, nerves and development were significantly expanded, revealing the potential genomic basis for the polyphagia of C. pallens and its role as an excellent biocontrol agent. This high-quality genome of C. pallens will provide an important genomic resource for future population genetics, evolutionary and phylogenetic investigations of Chrysopidae as well as comparative genomic studies of Neuropterida and other insects.

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. In this study, we first present robust estimator for the time to the most recent common ancestor (TMRCA) and the mutation rate, and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2. The mutation rate is inferred to be 8.69 × 10-4 per site per year with a 95% confidence interval (CI) of [8.61 × 10-4, 8.77 × 10-4], and the TMRCA of the samples inferred to be Nov 28, 2019 with a 95% CI of [Oct 20, 2019, Dec 9, 2019]. The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market. We further demonstrate that genetic polymorphism patterns, including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters, are similar to those caused by evolutionary forces such as natural selection. Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2. Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.

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. Built on this conception, we develop a computational approach that is capable of constructing ancestry informative panels from multi-population genome-wide SNP data efficiently. We evaluated the performance of the method by comparing the panel size and membership inference accuracy of the constructed SNP panels to panels selected through empirical procedures in previous studies. For the membership inference of population groups including Asian, European, African, East Asian and Southeast Asian, a 36-SNP panel developed by our approach has an overall accuracy of 99.07%, and a 21-SNP subset of the panel has an overall accuracy of 95.36%. In comparison, an existing panel requires 74 SNPs to achieve an accuracy of 94.14% on the same set of population groups. We further apply the method to four subpopulations within Europe (Finnish, British, Spanish and Italian); a 175-SNP panel can discriminate individuals of those European subpopulations with an accuracy of 99.36%, of which a 68-SNP subset can achieve an accuracy of 95.07%. We expect our method to be a useful tool for constructing ancestry informative markers in forensic genetics.

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 (dcos) and coalescence distance (dcoal) respectively, to infer surnames from Y-STR profiles. We also survey Y-STR variations at 15 loci for 19,009 individuals of Shandong Province in China. For a total of 266 surnames included in the data set, our methods can pinpoint to a single surname with an average accuracy of 65%, and with an average accuracy higher than 80% when providing >4 candidate surnames. We also demonstrate that increasing the sample size of surnames and the number of STR loci improves the accuracy of surname inference. Our results indicate that the 15 non-duplicated Y-STR loci contain information from which surname can be reliably inferred for Chinese populations, showing a promising application in forensics.

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 0.860, with the observed allele numbers varying from two to 25. Overall, there were no deviations from Hardy-Weinberg equilibrium and no observed linkage disequilibrium after Bonferroni correction. Cross-species amplification of these loci in Mesobuthus eupeus revealed that five loci can amplify successfully in this species. The polymorphic microsatellite DNA markers reported here should provide helpful means to address questions concerning phylogeographical patterns and evolutionary history of M. martensii and closely related species.