BMC Genomics最新文献

Background: Chemosensory perception plays a vital role in insect survival and adaptability, driving essential behaviours such as navigation, mate identification, and food location. This sensory process is governed by diverse gene families, including odorant-binding proteins (OBPs), olfactory receptors (ORs), ionotropic receptors (IRs), chemosensory proteins (CSPs), gustatory receptors (GRs), and sensory neuron membrane proteins (SNMPs). The oriental mole cricket (Gryllotalpa orientalis Burmeister), an invasive pest with an underground, phyllophagous lifestyle, causes substantial crop damage. This study characterizes the chemosensory gene repertoire of G. orientalis based on de novo genome assembly and transcriptomic analysis.

Results: We present a draft genome of G. orientalis at the scaffold level, spanning 2.94 Gb and comprising 10,497 scaffolds. This assembly encodes 19,155 protein-coding genes, including 158 chemosensory genes: 30 odorant receptors (ORs), 64 ionotropic receptors (IRs), ten gustatory receptors (GRs), 28 odorant-binding proteins (OBPs), 25 chemosensory proteins (CSPs), and a single sensory neuron membrane protein (SNMP). Expression analysis indicated that 71 chemosensory genes were actively expressed in the head, thorax, and legs, with ORs and OBPs showing higher expression in the head and legs. In contrast, GRs and IRs were predominantly expressed in the head.

Conclusions: This study provides the first comprehensive identification of chemosensory gene families in the G. orientalis genome, characterized as a scaffold-level draft genome. These findings provide a basis for future functional studies and highlight the role of chemoreception in the subterranean environment.

Background: Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due to its soluble dietary fiber β-glucan, a hemicellulose known to prevent cardio-vascular diseases. To maximize health benefits associated with the consumption of oat-based food products, breeding efforts have aimed at increasing the β-glucan content in oat groats. However, progress has been limited. To accelerate oat breeding efforts, we leveraged existing breeding datasets (1,230 breeding lines from South Dakota State University oat breeding program grown in multiple environments between 2015 and 2022) to conduct a genome-wide association study (GWAS) to increase our understanding of the genetic control of beta-glucan content in oats and to compare strategies to implement genomic selection (GS) to increase genetic gain for β-glucan content in oat.

Results: Large variation for β-glucan content was observed with values ranging between 3.02 and 7.24%. An independent GWAS was performed for each breeding panel in each environment and identified 22 loci distributed over fourteen oat chromosomes significantly associated with β-glucan content. Comparison based on physical position showed that 12 out of 22 loci coincided with previously identified β-glucan QTLs, and three loci are in the vicinity of cellulose synthesis genes, Cellulose synthase-like (Csl). To perform a GWAS analysis across all breeding datasets, the β-glucan content of each breeding line was predicted for each of the 26 environments. The overall GWAS identified 73 loci, of which 15 coincided with loci identified for individual environments and 37 coincided with previously reported β-glucan QTLs not identified when performing the GWAS in single years. In addition, 21 novel loci were identified that were not reported in the previous studies. The proposed approach increased our ability to detect significantly associated markers. The comparison of multiple GS scenarios indicated that using a specific set of markers as a fixed effect in GS models did not increase the prediction accuracy. However, the use of multi-environment data in the training population resulted in an increase in prediction accuracy (0.61-0.72) as compared to single-year (0.28-0.48) data. The use of USDA-SoyWheOatBar-3 K genotyping array data resulted in a similar level of prediction accuracy as did genotyping-by-sequencing data.

Conclusion: This study identified and confirmed the location of multiple loci associated with β-glucan content. The proposed genomic strategies significantly increase both our ability to detect significant markers in GWAS and the accuracy of genomic predictions. The findings of this study can be useful to accelerate the genetic improvement of β-glucan content and other traits.

Background: Rising seawater temperatures increasingly threaten coral reefs. The ability of coral larvae to withstand heat is crucial for maintaining reef ecosystems. Although several studies have investigated coral larvae's genetic responses to thermal stress, most relied on pooled sample sequencing, which provides population-level insights but may mask individual genotype variability. This study uses individual larval sequencing to investigate genotype-specific responses to heat stress and the selective pressures shaping their genomes, offering finer resolution and deeper insights.

Results: This study investigates the larval response to heat stress before acquiring symbiotic algae, aiming to elucidate the relationship between coral genetic diversity and heat stress. Larvae sourced from eight Acropora digitifera colonies were subjected to ambient temperature (28 °C) and heat conditions (31 °C). The impact of heat stress on larval genetic diversity was assessed through sequencing. While overall genetic diversity, represented by π, did not significantly differ between the control and heat-exposed groups, Tajima's D differed, indicating different selective pressures in each group. The genomic regions under higher and lower Tajima's D were not broadly shared among control and head conditions, implying that selective pressures operated in distinctive manners. Many larval protein-coding sequences were identified in this genomic region, and the codon evolution of many of these genes showed signs of positive selection. These results highlight the complex selective pressures on coral larvae under different temperatures. The genes showing signs of positive selection in response to heat stress may have also been influenced by historical temperature fluctuations, as suggested by their association with loci identified during Acroporid speciation. These loci under codon-level positive selection during speciation highlight the potential role of genetic diversity in shaping adaptation to environmental changes over evolutionary timescales.

Conclusion: These findings underscore the significance of genetic diversity in coral reproduction for maintaining reef ecosystems. They also indicate that even minor heat stress can exert significant selective pressure, potentially leading to profound implications for coral reef ecosystems. This research is crucial for understanding the impact of rising seawater temperatures on coral reefs.

Background: Gyrodactylus von Nordmann, 1832, a genus of viviparous parasites within the family Gyrodactylidae, contains one of the largest nominal species in the world. Gyrodactylus pseudorasborae Ondračková, Seifertová & Tkachenko, 2023 widely distributed in Europe and China, although its mitochondrial genome remains unclear. This study aims to sequence the mitogenome of G.pseudorasborae and clarify its phylogenetic relationship within the Gyrodactylidea. The mitochondrial genome of G. pseudorasborae was amplified in six parts from a single parasite, sequenced using primer walking, annotated and analyzed using bioinformatic tools.

Results: The mitochondrial genome of G. pseudorasborae is 14,189 bp in length, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and two major non-coding regions (NCR: NC1 and NC2). The overall A + T content of the mitogenome is 73.1%, a medium content compared with all reported mitochondrial genomes of monogeneans. The mitogenome of G. pseudorasborae presents a clear bias in nucleotide composition with a negative AT skew and a positive GC skew except for NCR. All tRNAs have the typical cloverleaf secondary structure except for tRNA^Cys, tRNA^Ser1, and tRNA^Ser2, which lack the dihydrouridine (DHU) arm. Furthermore, one repetitive non-coding region of 32 bp repeats occurred in the NC1 region with poly-T stretch, stem-loop structure, and TAn motif. The gene order is identical to the mitochondrial genomes reported from other Gyrodactylus species except Gyrodactylus nyanzae Paperna, 1973 and Gyrodactylus sp. FZ-2021. Phylogenetic analyses show that G. pseudorasborae and Gyrodactylus parvae You, Easy & Cone, 2008 cluster together with high nodal support based on 12 PCGs sequences and amino acid sequences, Gyrodactylidae forms independent monophyletic clade within Gyrodactylidea.

Conclusion: Both the mitochondrial genome and phylogenetic analyses support G. pseudorasborae is a member of the genus Gyrodactylus and Gyrodactylidae forms an independent monophyletic clade within Gyrodactylidea. Furthermore, the mitochondrial genome of G. pseudorasborae is the shortest in the Gyrodactylidea species compared with size differences in NCR.

Background: Identifying markers or genes crucial for growth traits in Zhongwei goats is pivotal for breeding. Pinpointing genetic factors linked to body size gain enhances breeding efficiency and economic value. In this study, we used the MGISEQ-T7 platform to re-sequence 240 Zhongwei goats (133 male; 107 female) belonging to 5 metrics of growth traits at different growth stages (40 days and 6 months, here in after referred to as 40d and 6 m), namely, Body Weight (BW), Body Height (BH), Body Length (BL), Chest Circumference (CC), Tube Circumference (TC) were examined. A Genome-wide association study (GWAS) was conducted to identify candidate genes associated with the five indicators of body conformation traits, thereby establishing a foundation for subsequent investigations into the biological functions of these genes.

Results: A total of 19.89 Tb of raw data was generated with an average sequencing depth of about 20×. After quality control, 15,958,716 SNPs were available for the analysis. A total of 342 genome-wide significant SNPs were obtained. Among them, in the two physiological stages of 40d and 6 m, 147 and 32 SNPs were significantly associated with BW; 1 and 4 SNPs were significantly associated with BH; 19 and 6 SNPs were significantly associated with BL; 33 and 64 SNPs were significantly associated with CC, 34 and 2 SNPs were significantly associated with TC. These SNPs were annotated to 425 candidate genes. Finally, A total of 39 candidate genes are closely related to biological processes such as skeletal muscle development, skeletal formation, carcass quality, and embryonic development, where ADIPOQ, CCDD39, PTPRT, ZNF215, VRTN, ABCD4, DLST, ADAMTS2, ROBO1, AKAP13, AQPI, SOX2, and AHSG were identified as an important component of the genetic framework that may control somatic conformational traits in Zhongwei goats. which warrants further investigation and review. We verified the polymorphism of 11 SNPs by KASP, and found that Chr13_g.11,700,438 A > G, Chr15_g.37,120,328 A > G, Chr6_g.7,209,383 C > T, Chr20_g.51277932T > A, Chr19_g.17,078,199 A > G, and Chr1_g.79,943,276 C > T were significantly genotyped in verified populations (P < 0.001).

Conclution: It is the first GWAS study to analyze genomic data from 40d and 6 m of Zhongwei goats to understand the molecular genetic mechanisms of growth. Our research identified a series of SNPs and candidate genes associated with growth traits, which could assist us in developing the meat production trait in Zhongwei goats.

Background: Muscle and adipose tissue are the most critical indicators of beef quality, and their development and function are regulated by noncoding RNAs (ncRNAs). However, the differential regulatory mechanisms of ncRNAs in muscle and adipose tissue remain unclear.

Results: In this study, 2,343 differentially expressed mRNAs (DEMs), 235 differentially expressed lncRNAs (DELs), 95 differentially expressed circRNAs (DECs) and 54 differentially expressed miRNAs (DEmiRs) were identified in longissimus dorsi muscle (LD), subcutaneous fat (SF) and perirenal fat (VF) in Qinchuan beef cattle. The results of functional enrichment analysis showed that DEMs, DELs, DECs and DEmiRs were enriched in biological processes related to development and function of muscle and fat deposition, including skeletal muscle contraction, muscle organ development, PPAR signaling pathway, fatty acid metabolism and MAPK signaling pathway. Based on the competing endogenous RNA (ceRNA) regulatory mechanism, we constructed a lncRNA/circRNA-miRNA-mRNA network consisting of 6 circRNAs, 5 lncRNAs, 6 miRNAs and 27 mRNAs. Among them, 55 ceRNA axes were involved, including circRNA12990 - bta-miR-133a_L-1R + 1 - MYO6/ZEB2, circRNA2893/MSTRG.28538.1/MSTRG.11613.4 - pma-miR-145-5p_R + 2 - EYA4 and MSTRG.26982.1 - bta-let-7e_R + 1 - RBM40.

Conclusions: This study identified a group of differentially expressed mRNAs, lncRNAs, circRNAs and miRNAs between muscle and adipose tissue and constructed a potential ceRNA regulatory network, which may serve as a foundation for studying the differential regulatory roles of ncRNAs in the development and function of muscle and adipose tissue.

Cold stress in winter is one of the most severe abiotic stresses on plant growth and flourishing, and the selection of cold tolerant genotypes is an important strategy to ensure the safety of plant growth and development. Cyclocarya paliurus, a diclinous and versatile tree species originally in subtropical regions, has been introduced and cultivated in the warm temperate zone of China to meet the increasing market demand for its leaf yield. However, information regarding its cold tolerance remains limited. Based on the ploidy identification of tested materials, an imitation experiment was conducted to investigate the variation in freezing injury index and expression of the CpaWRKY family members in diploid and tetraploid C. paliurus seedlings. The results indicated a significant difference in freezing injury index between diploids and tetraploids under the imitating temperature of southern warm temperate zone, with diploids showing better cold tolerance than the tetraploids. A total of 88 CpaWRKY genes were identified from the C. paliurus genome, and RNA-Seq results showed significant differences in WRKY gene expression in C. paliurus under cold stress. Correlation analysis between differentially expressed genes and freezing injury index suggested that CpaWRKY14, CpaWRKY26 and CpaWRKY86 play essential roles in the diploids to respond to cold stress. In contrast, the major genes involved in the cold stress response in tetraploids were CpaWRKY14, CpaWRKY60, CpaWRKY63 and CpaWRKY81. Moreover, CpaWRKY14 expression was considerably higher in diploids compared to tetraploids. The results from this study not only enhance our comprehension of the role of the CpaWRKY genes in cold stress, but also provide a foundation for the genetic improvement of C. paliurus.

Background: Megalobrama amblycephala presents unsynchronized growth, which affects its productivity and profitability. The liver is essential for substance exchange and energy metabolism, significantly influencing the growth of fish.

Results: To investigate the differential metabolites and genes governing growth, and understand the mechanism underlying their unsynchronized growth, we conducted comprehensive transcriptomic and metabolomic analyses of liver from fast-growing (FG) and slow-growing (SG) M. amblycephala individuals. A total of 2,097 differentially expressed genes (DEGs) were identified between FG and SG, with 830 genes exhibiting significantly higher expression level in FG. KEGG and GO enrichment analysis indicated that the DEGs with higher expression level were significantly correlated with insulin signaling pathway, steroid hormone and lipid metabolism related pathway (PPAR signaling pathway and fatty acid degradation). In the metabolomic analysis, 224 differentially expressed metabolites (DEMs) were detected, of which 128 were significantly more abundant in FG. These more abundant DEMs were prominently enriched in pathways associated with cell proliferation and energy metabolism (Oxidative phosphorylation, mTOR signaling pathway and FoxO signaling pathway). In addition, DEGs and DEMs in adenosine diphosphate (ATP) hydrolysis activity and associate with fatty acid metabolism, glucose metabolism, and amino acid metabolism pathways were both found in the transcriptomic and metabolomic integrated data. These findings suggest that the large amounts of energy generated by fatty acid, glucose metabolism and other energy metabolism pathway promote the rapid growth of FG.

Conclusions: This research is the first to integrate metabolomic and transcriptomic analyses of liver to identify key genes, metabolites, and pathways to uncover the molecular and metabolic mechanisms of unsynchronized growth in M. amblycephala. The identified metabolic and genes can be potential targets for selective breeding programs to improve growth performance in aquaculture.

Age-related muscle wasting, sarcopenia is an extensive loss of muscle mass and strength with age and a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to survey the global changes in protein-coding gene expression occurring in skeletal muscle with age. Caloric restriction (CR) is a known prophylactic intervention against sarcopenia. Therefore, total RNA was isolated from the muscle tissue of both rats fed ad libitum and CR rats. RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. This revealed the functional pathways most activated by both ageing and CR, as well as the key "hub" proteins involved in their activation.RNA-seq revealed 442 protein-coding genes to be upregulated and 377 to be downregulated in aged muscle, compared to young muscle. Upregulated genes were commonly involved in protein folding and immune responses; meanwhile, downregulated genes were often related to developmental biology. CR was found to suppress 69.7% and rescue 57.8% of the genes found to be upregulated and downregulated in aged muscle, respectively. In addition, CR uniquely upregulated 291 and downregulated 304 protein-coding genes. Hub genes implicated in both ageing and CR included Gc, Plg, Irf7, Ifit3, Usp18, Rsad2, Blm and RT1-A2, whilst those exclusively implicated in CR responses included Alb, Apoa1, Ambp, F2, Apoh, Orm1, Mx1, Oasl2 and Rtp4. Hub genes involved in ageing but unaffected by CR included Fgg, Fga, Fgb and Serpinc1. In conclusion, this comprehensive RNA sequencing study highlights gene expression patterns, hub genes and signalling pathways most affected by ageing in skeletal muscle. This data may provide the initial evidence for several targets for potential future therapeutic interventions against sarcopenia.

Background: Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far.

Results: Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas.

Conclusion: This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks.