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Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine–Cytosine content of 46.4%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at − 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications. [ABSTRACT FROM AUTHOR]

Ammopiptanthus mongolicus, a traditional ethnic medicinal herb, is a rare broad-leaved evergreen shrub in the arid region of central Asia that can survive under extremely low temperatures during winter. In this study, we investigated the cold stress response of A. mongolicus leaves using physiological and proteomic approaches. Cold stress treatment increased the relative electrolyte leakage, proline, and soluble sugar levels and decreased the chlorophyll content in A. mongolicus leaves. Moreover, 93 differentially abundant proteins (DAPs) were identified using two-dimensional electrophoresis, of which 79 were further confirmed via tandem mass spectrometric analysis. The predicted functions of DAPs were mainly associated with photosynthesis in chloroplasts, reactive oxygen species scavenging, defense, and protein synthesis, folding, and degradation. A. mongolicus chitinase A (AmCHIA) is a cold-induced apoplast protein whose transcription is upregulated under cold, osmotic, high-salinity, and mechanical stresses. Recombinant AmCHIA expressed in Escherichia coli exhibits chitinase activity. Here, AmCHIA expression enhanced the cold tolerance of E. coli cells, suggesting that it may contribute to the cold adaptation of A. mongolicus after cold treatment. The present study not only provides important data for understanding the cold stress responses in plants but also serves as a basis for further exploration of the biological functions of cold-induced proteins in A. mongolicus using genetic approaches. [ABSTRACT FROM AUTHOR]

Bactrian camels (Camelus bactrianus) are highly adapted to the desert and semi-desert environments of Asia and developed unique physiological adaptations to cold, heat, drought, and nutrient-poor conditions. These animals are an ideal model for studying desert adaptation. However, the transcriptome of different Bactrian camel tissues has not been profiled. This study performed a comprehensive transcriptome analysis of nine fetal and adult tissues. A total of 20,417 coding genes were identified, and 2.4 billion reads were generated. Gene expression and functional analyses revealed that approximately 50% of the identified genes were ubiquitously expressed, and one-third were tissue-elevated genes, which were enriched in pathways related to the biological functions of the corresponding tissue. Weighted gene co-expressed network analysis (WGCNA) identified four modules—fat metabolism, water balance, immunity, and digestion—and several hub genes, including APOA1, TMEM174, CXCL12, and MYL9. The analysis of differentially expressed genes (DEGs) between fetal and adult tissues revealed that downregulated genes were enriched in tissue development, whereas upregulated genes were enriched in biological function in adult camels. DEGs in the hump were enriched in immune-related pathways, suggesting that this tissue is involved in immunity. This study is the first to generate a transcriptome atlas of major tissues in Bactrian camels and explores the genes potentially involved in the adaptation to desert environments. [ABSTRACT FROM AUTHOR]

Environmental adaptation of crops is essential for reliable agricultural production and an important breeding objective. Genebanks provide genetic variation for the improvement of modern varieties, but the selection of suitable germplasm is frequently impeded by incomplete phenotypic data. We address this bottleneck by combining a Focused Identification of Germplasm Strategy (FIGS) with core collection methodology to select soybean (Glycine max) germplasm for Central European breeding from a collection of >17,000 accessions. By focussing on adaptation to high‐latitude cold regions, we selected an "environmental precore" of 3,663 accessions using environmental data and compared the Donor opulation of Environments (DPE) in Asia and the Target Population of Environments (TPE) in Central Europe in the present and 2070. Using single nucleotide polymorphisms, we reduced the precore into two diverse core collections of 183 and 366 accessions to serve as diversity panels for evaluation in the TPE. Genetic differentiation between precore and non‐precore accessions revealed genomic regions that control maturity, and novel candidate loci for environmental adaptation, demonstrating the potential of diversity panels for studying adaptation. Objective‐driven core collections have the potential to increase germplasm utilization for abiotic adaptation by breeding for a rapidly changing climate, or de novo adaptation of crops to expand cultivation ranges. [ABSTRACT FROM AUTHOR]

Tolerance to low temperature can be enhanced by pre-exposure to low, non-harmful temperatures, a process known as acclimation. The effects of acclimation on chilling tolerance in species from tropical and subtropical regions are not well understood. Therefore, we investigated whether acclimation improved chilling tolerance at the plumule and seedling stages in Asian rice. A comparison of the effect of acclimation between chilling tolerance scores from a tolerant (A58) and a susceptible (W107) strain demonstrated that acclimation enhances chilling tolerance especially in the tolerant strain, indicating that considerable genetic variation in acclimation capacity exists. The genetic variation in chilling tolerance in acclimated plants was investigated using 57 strains derived from cultivated ( Oryza sativa L. ssp. japonica and ssp. indica) and wild ( O. rufipogon Griff.) rice. The genetic differentiation of the japonica and indica subspecies of cultivated rice with regard to chilling tolerance was more prominent in the presence than in the absence of acclimation. Furthermore, latitudinal clines for chilling tolerance were observed in both acclimated plumules and seedlings of wild rice, whereas without acclimation, a latitudinal cline was observed only at the plumule stage. This suggests that acclimation capacity, as well as intrinsic chilling tolerance, might contribute to local adaptation. QTLs involved in acclimated chilling tolerance at the plumule stage are different from those involved in intrinsic chilling tolerance. The present results indicate that the maximum genetic potential for chilling tolerance is achieved by acclimation, giving cautions for evaluation of genetic resources in rice. [ABSTRACT FROM AUTHOR]

Ticks are a large group of blood-feeding arthropods that transmit multiple human and animal pathogens and are hence of importance to public health. The tick Haemaphysalis longicornis is associated with the transmission of multiple human pathogens in Asia, and recently found invading to the United States. Here, we report the sequencing, assembly and annotation of the 3.16 gigabase genome of this species, which is larger than the previous assembled one. The present Haemaphysalis longicornis genome was characterized by 6519 scaffolds, 24,189 protein-coding genes and a high proportion of simple sequence repeats (54.72%). By genomic assembly and comparative genomic analysis, we characterized the key genes that play essential roles in iron metabolism, detoxification, and freeze tolerance of H. longicornis. Furthermore, a total of 79 endogenous viral elements were identified within the genome, which might have had a considerable impact on its evolution. Decoding the H. longicornis genome not only provides insight into the genetic underpinnings of specific biological processes but also offers the basis for the subsequent integrated control of ticks and tick-borne diseases. • A high quality of 3.16 gigabase genome of Haemaphysalis longicornis were assembled. • The key genes mediating the requisite biological traits of H. longicornis were characterized. • A total of 79 endogenous viral elements were identified within the H. longicornis genome. • The genome annotation are useful for future control of ticks and tick-borne diseases. [ABSTRACT FROM AUTHOR]

The Asian corn borer (ACB) is the most devastating pest on maize in the western Pacific region of Asia. Despite broad interests in insecticide resistance, seasonal adaptation, and larval color mimicry regarding the ACB system, lacking of reference genomic information and a powerful gene editing approach have hindered the in-depth studies of these aspects. Here we present a 455.7 Mb draft genome of ACB with 98.4% completeness. Comparative genomics analysis showed an evident expansion in gene families of gustatory receptors (105), which is related to polyphagous characteristics. Based on the comparative transcriptome analysis of resistant and susceptible ACB against Bt Cry1Ab toxin, we identified 26 genes related to Cry1Ab resistance. Additionally, transcriptomics of insects exposed to conditions of low temperature and diapause (LT) vs. room temperature and diapause (RT) provided insights into the genetic mechanisms of cold adaptation. We also successfully developed an efficient CRISPR/Cas9-based genome editing system and applied it to explore the role of color pattern genes in the ecological adaptation of ACB. Taken together, our study provides a fully annotated high-quality reference genome and efficient gene editing system to realize the potential of ACB as a study system to address important biological questions such as insecticide resistance, seasonal adaptation, and coloration. These valuable genomic resources will also benefit the development of novel strategies for maize pest management. [Display omitted] •A draft genome of the Asian corn borer (ACB) is presented with full annotation. •Multi-omics analysis provided important insights into host adaptation and Bt insecticide resistance. •Gene families associated with seasonal and color adaptation were analyzed. •A CRISPR/Cas9-based gene editing system was established using the color patterning gene Ofyellow. [ABSTRACT FROM AUTHOR]

Mangrove forests growing at the poleward edges of their geographic distribution are occasionally subject to freezing (<0 °C) and cold wave (>0 °C) events. Cold wave effects on mangrove trees are well documented and adaptation to cold stress has been reported for local mangrove populations in the North Atlantic. However, there is less understanding of effects of cold waves on mangroves in the northern Pacific, especially at the regional scale. Moreover, it is unclear if cold tolerant mangrove species of North Asia display variation in resistance to cold temperatures across their geographic distribution. Using a cold wave event that occurred in January 2021, we evaluated the effects of low temperatures on vegetation index (VI) change (relative to a recent five-year baseline) for mangrove forests dominated by Kandelia obovata (Rhizophoraceae) and Avicennia marina (Acanthaceaee) at the northern edge of their geographical range. We used two VIs derived from Sentinel-2 imagery as indicators for canopy health: the normalized difference infrared index (NDII) and the chlorophyll red-edge index (ChlRE), which reflect forest canopy water content and chlorophyll concentration, respectively. We isolated the cold wave effects on the forest canopy from phenology (i.e., cold wave induced deviation from a five-year baseline) and used multiple linear regression to identify significant climatic predictors for the response of mangrove forest canopy VI change to low temperatures. For areas where the cold wave resulted in temperatures <10 °C, immediate decreases in both VIs were observed, and the VI difference relative to the baseline was generally greater at 30-days after the cold wave than when temperatures initially recovered to baseline values, showing a slight delay in VI response to cold wave-induced canopy damage. Furthermore, the two VIs did not respond consistently suggesting that cold-temperature induced changes in mangrove canopy chlorophyll and water content are affected independently or subject to differing physiological controls. Our results confirm that local baseline (i.e., recent past) climate predicts canopy resistance to cold wave damage across K. obovata stands in the northern Pacific, and in congruence with findings from New World mangroves, they imply geographic variation in mangrove leaf physiological resistance to cold for Northern Pacific mangroves. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, we investigated the liver transcriptomic responses of pearl gentian grouper towards cold stress. Some cold-related key genes and biological pathways were screened, of which energy-related metabolic pathways and genes had higher expression levels under cold stress. This suggested that energy homeostasis plays a crucial role in the physiological adjustments of pearl gentian grouper when exposed to the cold stress environment. Our results will expedite the understanding of different fishes adaptive mechanisms to profound environmental temperature changes and provide insights into the molecular breeding of cold-tolerant pearl gentian grouper varieties. Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress. [ABSTRACT FROM AUTHOR]

When, how, and following which paths hominins created the innovations that allowed them to colonize regions of the planet that were not suited to their thermal physiology is still a matter of inquiry. In this paper, we elaborate a theoretical framework to investigate the origin and diversification of bone needles, summarize the evidence for their emergence, create a large database of their morphometric and stylistic characters, and present results of the study of an exceptionally well-preserved collection of needles from Shuidonggou Locality 12 (SDG12), a site located in the Ningxia Hui Autonomous Region, Northern China, dated to ca. 11.2 ka BP. Bone needles are reported from 271 sites and 355 archaeological layers. Revision of the evidence shows they represent an original cultural innovation that emerged in Eurasia between 45-40 ka BP. Size differences between the earliest known specimens, found in Siberia and China, indicate needles may have been invented independently in these two regions. Needles from Eastern Europe may represent either an independent invention or a geographic extension of earlier Siberian and Caucasian sewing traditions. In Western Europe, needles appear during the Solutrean. The wider size range characteristic of Magdalenian specimens supports the idea that needles of different sizes were used in a variety of tasks. In China, the robust sub-circular needles found at sites dated between 35-25 ka BP are followed, between 26-23 ka BP, by small flat needles, which may represent an innovation associated with the microblades/microcores toolkit. At SDG12, technological, functional, and morphometric analyses of finished needles and manufacturing by-products identify two previously undetected reduction sequences for the production of needles of different size and, probably, function. The bone needles found at Paleoindian sites are the smallest and reflect a never previously achieved mastery in the production of such tools., (Copyright © 2018 Elsevier Ltd. All rights reserved.)