摘要: Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species; however, their roles in gene transcription,especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily(LTR4C＿SS), containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat(LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.

摘要: We examined the global biogeography of the Scytodes thoracica group of spitting spiders based on 23 years of sampling at the species level(61 species in the thoracica group and 84 species of Scytodes) using DNA data from six loci. Our results indicated that the thoracica group initially dispersed from Southeast Asia to East Africa between 46.5 and 33.0 million years ago, and dispersal events intensified between Southeast/South Asia and East/South Africa from the early to late Miocene. The timing of these events indicates that Asian-African faunal exchange of the thoracica group was driven by the Indian monsoon, and the pattern of dispersal suggests that colonialization took root when the Indian monsoon shifted from a North-South direction to an East-West direction from the middle Eocene.

摘要: The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements,usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats(IRs) cause significant gene rearrangements of protein coding genes(PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower d N/d S ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.UnlikeconservedPCGsandrRNAswhose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.

摘要: Omega-3 polyunsaturated fatty acids(n-3 PUFAs),particularly docosahexaenoic acid(22:6n-3, DHA), play crucial roles in the reproductive health of vertebrates,includinghumans.Nevertheless,theunderlying mechanism related to this phenomenon remains largely unknown. In this study, we employed two zebrafish genetic models, i.e., elovl2-/-mutant as an endogenous DHAdeficient model and fat1(omega-3 desaturase encoding gene) transgenic zebrafish as an endogenous DHA-rich model, to investigate the effects of DHA on oocyte maturation and quality. Results show that the elovl2-/-mutants had much lower fecundity and poorer oocyte quality than the wild-type controls, while the fat1 zebrafish had higher fecundity and better oocyte quality than wildtype controls. DHA deficiency in elovl2-/-embryos led to defects in egg activation, poor microtubule stability, and reduced pregnenolone levels. Further study revealed that DHA promoted pregnenolone synthesis by enhancing transcription of cyp11a1, which encodes the cholesterol side-chaincleavageenzyme,therebystabilizing microtubule assembly during oogenesis. In turn, the hypothalamic-pituitary-gonadal axis was enhanced by DHA. In conclusion, using two unique genetic models, our findings demonstrate that endogenously synthesized DHA promotes oocyte maturation and quality by promoting pregnenolone production via transcriptional regulation of cyp11a1.

摘要: Monitoring the prevalence of antimicrobial resistance genes(ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72–0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

摘要: Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster(Crassostrea ariakensis) is an economically and ecologically important species in China. In the present study, RNA sequencing(RNA-seq) and assay for transposase-accessible chromatin using sequencing(ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents. Analysis identified9 ?483 differentially expressed genes(DEGs) and 7 ?215genes with significantly differential chromatin accessibility(DCAGs) were obtained, with an overlap of 2 ?600 genes between them. Notably, a significant proportion of these genes were enriched in pathways related to glycogen metabolism, including “Glycogen metabolic process” and“Starch and sucrose metabolism”. In addition, genomewide association study(GWAS) identified 526 single nucleotide polymorphism(SNP) loci associated with glycogen content. These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C. ariakensis.

摘要: A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1?633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders(Calcaxonia, Holaxonia,Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity(ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous(Ka) to synonymous(Ks) substitution ratio(Ka/Ks) suggested that the 14 protein-coding genes(PCGs) were under purifying selection, likely due to specific deep-sea environmental pressures. Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b) and DNA mismatch repair protein(mutS) may be influenced by environmental factors in the context of deep-sea species formation. This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

摘要: DEAR EDITOR,The Laosicheng site in Yongshun County, Hunan Province,China, plays an important role in elucidating the animal population composition of the region prior to the middle Qing Dynasty (approximately 300 years ago). This site has yielded a substantial number of animal bones, 11?960 of which have been identified to the species level, serving as direct evidence of ancient animal populations (Hunan Provincial Institute of Cultural Relics and Archaeology, 2018).

摘要: To halt biodiversity loss,threatened species are often selected as targets for conservation actions.However,whether most threatened species receive sufficient research effort remains unknown.Low research and public attention of threatened species would hinder the implementation of effective conservation actions.Therefore,it is urgent to assess both research effort and species extinction risk simultaneously to provide critical information for targeted conservation practices.Here,we evaluated research effort of extant bird species worldwide(n=10,904) by searching the number of all publications and those focused on conservation in Scopus database for each species,and investigated key determinants of research effort.We found that although the median value of publications of threatened species was significantly higher than that of non-threatened species,47.4% of threatened species had less than 3 publications,and 73.8% had less than 10 publications,indicating low research effort of most threatened species.Although research effort was positively related to extinction risk,research effort was mainly associated with human-related variables,with birds described earlier and occurred in developed regions receiving higher research effort.In comparison,extinction risk was mainly associated with biological attributes,with large-sized and narrow-distributed species being more likely to be threatened.Our finding suggests that research effort of species can provide complementary information for current conservation strategies designed for threatened species,and we urge that many recently discovered and narrowly distributed species in less developed regions require more research and conservation attention.

摘要: The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines. However, few studies have investigated intraspecies mitogenomic variation. In this study, 69 mitogenomes of the Black-throated Tit(Aegithalos concinnus) were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length, gene and nucleotide composition, codon usage, and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes. Yet, all the individuals from the subspecies A. c. iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies. Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes, whereas only four lineages were observed when using the duplicate control regions. Most interestingly, each lineage had both copies of the control regions of the comprising individuals, indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages. This suggested the control regions had undergone concerted evolution. The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages, as well as the underlying evolutionary processes. Our findings call for more research on intraspecies mitogenomic variation.