BMC Genomics最新文献

Background: The diversity-generating retroelements (DGRs) are a family of genetic elements that can produce mutations in target genes often related to ligand-binding functions, which possess a C-type lectin (CLec) domain that tolerates massive variations. They were first identified in viruses, then in bacteria and archaea from human-associated and environmental genomes. This DGR mechanism represents a fast adaptation of organisms to ever- changing environments. However, their existence, phylogenetic and structural diversity, and functions in a wide range of environments are largely unknown.

Results: Here we present a study of DGR systems based on metagenome-assembled genomes (MAGs) from host-associated, aquatic, terrestrial and engineered environments. In total, we identified 861 non-redundant DGR-RTs and ~ 5.7% are new. We found that microbes associated with human hosts harbor the highest number of DGRs and also exhibit a higher prevalence of DGRs. After normalizing with genome size and including more genome data, we found that DGRs occur more frequently in organisms with smaller genomes. Overall, we identified nine main clades in the phylogenetic tree of reverse transcriptases (RTs), some comprising specific phyla and cassette architectures. We identified 38 different cassette patterns and 6 of them were shown in at least 10 DGRs, showing differences in terms of the numbers, arrangements, and orientations of their components. Finally, most of the target genes were related to ligand-binding and signaling functions, but we discovered a few cases in which the VRs were situated in domains different from the CLec.

Conclusions: Our research sheds light on the widespread prevalence of DGRs within environments and taxa, and supports the DGR phylogenetic divergence in different organisms. These variations might also occur in their structures since some cassette architectures were common in specific underrepresented phyla. In addition, we suggest that VRs could be found in domains different to the CLec, which should be further explored for organisms in scarcely studied environments.

Background: Bovine mastitis significantly impacts the dairy industry, causing economic losses through reduced milk production, lower milk quality, and increased health risks, and early detection is critical for effective treatment. This study analyzed milk electrical conductivity data from 9,846 Chinese Holstein cows over a two-year period, collected during three daily milking sessions, alongside smart collar data and dairy herd improvement test results. The aim was to conduct a comprehensive genetic analysis and assess the potential of milk electrical conductivity as a biomarker for the early detection of bovine subclinical mastitis.

Results: The results revealed significant phenotypic and strong genetic correlations (-0.286 to 0.457) between milk electrical conductivity, somatic cell score, milk yield, activity quantity, and milking speed. Logistic regression models yielded area under the curve values ranging from 0.636 to 0.697 and odds ratio values from 9.70 to 10.69, demonstrating a certain predictive capability of milk electrical conductivity for identifying subclinical mastitis. Various factors influencing milk electrical conductivity, including lactation stage, environmental conditions, age at first calving, parity, and body condition score, were identified. The random regression model demonstrated moderate to high heritability of milk electrical conductivity (0.458 to 0.487), particularly during the early to mid-lactation periods, with all estimates exceeding 0.35 However, after day 275 of lactation, the heritability decreased to below 0.2. Notably, shifts in genetic factors affecting milk components were observed around 60 and 270 days into lactation, with increased environmental sensitivity to milk electrical conductivity during these periods.

Conclusions: This study demonstrates that milk electrical conductivity is influenced by multiple factors, such as age at first calving, parity, and body condition score, and exhibits significant phenotypic associations with somatic cell score, milk yield, activity quantity, and milking speed. Although milk electrical conductivity showed moderate to high heritability and potential as a predictor for subclinical mastitis, its low genetic correlations with SCS limit its effectiveness as a standalone indicator. Future research should focus on combining EC with other indicators to improve the accuracy of mastitis detection.

Background: Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa.

Results: In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065, gene LOC110696037, gene LOC110736224, and gene LOC110705759, belonging to the bHLH, NF-YA, MYB, and FAR1 gene families, respectively.

Conclusions: These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance.

Background: Organization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown.

Results: We examined the genome organization of a Neurospora strain harboring a ~ 47.4 kilobase deletion within a temporarily silent, facultative heterochromatic region, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion minimally effects local chromatin structure or telomere clustering, the constitutive heterochromatin deletion alters local chromatin structure, the predicted three-dimensional chromosome conformation, and the expression of some genes, which are qualitatively repositioned into the nucleus center, while increasing Hi-C variability.

Conclusions: Our work elucidates how an individual constitutive heterochromatic region impacts genome organization and function. Specifically, one silent region indirectly assists in the hierarchical folding of the entire Neurospora genome by aggregating into the "typical" heterochromatin bundle normally observed in wild type nuclei, which may promote normal gene expression by positioning euchromatin in the nucleus center.

Background: In recent years, the total production of mud crab Scylla paramamosain has been declining, and the breeding areas are faced with land shortage and shortage of breeding production, which needs to be solved urgently. S. paramamosain can survive and grow in a wide range of salinities is an excellent variety suitable for saline-alkali water aquaculture. As a species with high economic value and strong adaptability to the environment, its cultivation under low salt conditions can not only improve the utilization efficiency of saline-alkali land, but also provide new possibilities for the sustainable development of aquaculture.

Results: A total of 248 different metabolites were identified by LC/GC-MS in the intestinal tract of S. paramamosain. These different metabolites were mainly concentrated in 'Lipids and lips-like molecules'. Among them, 112 metabolites are upregulated, and among these upregulated metabolites are mainly 'Fatty Acyls' and 'Glycerophospholipids'. The upregulation of these metabolites indicates an increase in lipid storage of S. paramamosain, which may increase the resistance of S. paramamosain to adverse environmental stress. Among them, 136 metabolic differentiates were down-regulated, mainly 'Carboxylic acids and derivatives'. The down-regulation of these organic acids may indicate that organic acids are used as energy sources for the immune response to long-term environmental stress.

Conclusion: Under long-term chloride type low-salt saline-alkali water stress, S. paramamosain will shift to another homeostasis for development.

Background: Locust outbreaks cause devastation and provide material for fundamental research. They associate with a case of phenotypic plasticity whereby the shift between the two extremes of the polyphenism (i.e., gregarious phase versus solitarious phase) affects behaviour as well as most aspects of the locusts' biology. The phenotypic changes imply changes in gene expression, the changes in behaviour characterize the locusts' phase change, and the changes in the Central Nervous System (CNS) control the changes in behaviour. Thus, understanding and tackling the phenomenon requires studying the gene expression changes that the locusts' CNS undergoes between phases. The genes that change expression the same way in different locusts would be ancestrally relevant for the phenomenon in general and some of those that change expression in a species-specific way would be relevant for the phenomenon in species-specific way.

Methods: Here, we use available raw sequencing reads to build transcriptomes and to compare the gene expression changes that the CNS of the two main pest locusts (Schistocerca gregaria and Locusta migratoria) undergo when they turn gregarious. The differentially expressed genes resulting from this comparative study were compared with the content of the L. migratoria core transcriptional phase signature genes database. Our aim is to find out about the species-specificity of the phenomenon, and to highlight the genes that respond in the same way in both species.

Results: The locust phase change phenomenon seems highly species-specific, very likely due to the inter-specific differences in the material used, and in the biology and life conditions of the different locust species. Research on locust outbreaks, gregariousness and swarming would therefore benefit from considering each locust species apart, and caution is needed when extrapolating results between species-as no species seems representative of all locust species. Still, the 109 genes and 39 non-annotated sequences that we found to change expression level the same way in the two main pest locusts, especially those previously reported as core transcriptional phase signature genes in L. migratoria's CNS-related tissues (10 and 1, respectively), provide material for functional testing in search for important genes to better understand, or to fight against locust outbreaks in a non-species-specific way. The large set of genes that respond in a species-specific way provide material for comparing, understanding and tackling the locust's phase change phenomenon in a species-specific way. The still uncharacterized transcripts that change expression either in a species-specific or the same way between the two species studied here provide material for gene discovery. Functional testing and confirmation are needed in all cases.

Background: Parasitic nematodes significantly undermine global human and animal health and productivity. Parasite control is reliant on anthelmintic administration however over-use of a limited number of drugs has resulted in escalating parasitic nematode resistance, threatening the sustainability of parasite control and underscoring an urgent need for the development of novel therapeutics. FMRFamide-like peptides (FLPs), the largest family of nematode neuropeptides, modulate nematode behaviours including those important for parasite survival, highlighting FLP receptors (FLP-GPCRs) as appealing putative novel anthelmintic targets. Advances in omics resources have enabled the identification of FLPs and neuropeptide-GPCRs in some parasitic nematodes, but remaining gaps in FLP-ligand libraries hinder the characterisation of receptor-ligand interactions, which are required to drive the development of novel control approaches.

Results: In this study we exploited recent expansions in nematode genome data to identify 2143 flp-genes in > 100 nematode species across free-living, entomopathogenic, plant, and animal parasitic lifestyles and representing 7 of the 12 major nematode clades. Our data reveal that: (i) the phylum-spanning flps, flp-1, -8, -14, and - 18, may be representative of the flp profile of the last common ancestor of nematodes; (ii) the majority of parasitic nematodes have a reduced flp complement relative to free-living species; (iii) FLP prepropeptide architecture is variable within and between flp-genes and across nematode species; (iv) FLP prepropeptide signatures facilitate flp-gene discrimination; (v) FLP motifs display variable length, amino acid sequence, and conservation; (vi) CLANS analysis provides insight into the evolutionary history of flp-gene sequelogues and reveals putative flp-gene paralogues and, (vii) flp expression is upregulated in the infective larval stage of several nematode parasites.

Conclusions: These data provide the foundation required for phylum-spanning FLP-GPCR deorphanisation screens in nematodes to seed the discovery and development of novel parasite control approaches.

Feather pecking (FP) is a repetitive behaviour in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviours seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behaviour (HFP or LFP). We integrate data on Differentially Methylated Regions (DMRs), Single Nucleotide Polymorphisms (SNPs), and Copy Number Variations (CNVs) in this controlled artificial selection process. Significant differences in behaviour, immunology, and neurology have been reported in these lines. We identified 710 SNPs in these lines that indicate new potentially important genes for FP such as TMPRSS6 (implicated in autism), and SST and ARNT2 (somatostatin function). CNV were the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP Quantitative Trait Loci (QTL) database revealed novel candidate genes for understanding repetitive behaviours, such as RTKN2, associated with Alzheimer's disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.

Background: Kinesin is a motor for microtubule-based motility. It plays a vital role in plant growth and development. The kinesin superfamily members are known mainly from Arabidopsis. Little research about kinesin superfamily has been conducted on hexploid wheat (Triticum aestivum L.). The functions of kinesins in wheat growth and development, regulation of cell division and response to stress are still unclear.

Results: In this study, we identified 155 kinesin (TaKIN) genes in wheat, which were divided into 10 families and some orphan genes via phylogenetic analysis. Less gene structural differences showed that TaKIN genes had redundant functions. The conserved domains of different family members were different, and some families might have some special functional domains. We found many cis-acting elements related to hormones (GA, Auxin, SA, MeJA), cell cycle and cell division in homeopathic elements of the TaKIN genes. Collinearity analysis showed that TaKIN genes were more conservative in monocotyledons. Expression level in different tissues at different stages suggested that TaKIN family may function during the whole growth and development process in wheat. It was worth noting there were quite different at gene expression level between physiological and heritable male sterile lines during the different stages of pollen development. The differential expression patterns of some TaKIN genes between male sterile line and maintainer line might be related to wheat male sterility. Furthermore, we also found TaKIN genes were involved in response to plant hormones and abiotic stress by stress assays.

Conclusions: The result is useful for further exploration of the molecular mechanism of kinesin genes in wheat male sterility and provides important information concerning response to plant hormones and abiotic stress caused by kinesin genes.