BMC Genomics最新文献

Foxtail millet (Setaria italica) is one of the most ancient cultivated cereal crops and is ideal for the functional genomics of the Panicoideae crops. In the present study, we generated an F₂ population consisting of 300 individuals by crossing an elite foxtail millet variety Jingu28 with a backbone line Ai88, and constructed a genetic linkage map with 213 published SSR markers and two InDel markers. Quantitative trait locus (QTL) mapping identified 46 QTL for 12 agronomic traits, including 13 major effect QTL. Meanwhile, 40 QTL controlling different traits formed 13 co-located QTL clusters. Moreover, one putative candidate gene Seita.9G020100 for qHD9-1 with conserved CCT motif and a gibberellin biosynthesis related GA20 oxidase gene Seita.5G404900 for qPH5-1 were identified based on homologous gene comparison. The 277 bp insertion/deletion on the promoter of Seita.9G020100 and the one-base (G) insertion/deletion in the third exon of Seita.5G404900 might be candidate functional sites. Furthermore, two markers (Ghd7InDel and GA20oxSTARP-1) were developed based on these two variation sites, respectively. These results will help to elucidate the genetic basis of important agronomic traits in foxtail millet and be useful for marker-assisted selection of varieties with ideal plant architecture and high yield potential.

Background: Staphylococcus aureus is an important pathogen that can colonize humans and various animals. However, the host-associated determinants of S. aureus remain uncertain, which leads to difficulties in inferring its host species and cross-species transmission. We performed a 3-stage genome-wide association study (discovery, confirming, and validation) to compare genetic variation between pig and human S. aureus, aiming to elucidate the host-specific genetic elements (k-mers).

Results: After 3-stage association analyses, we found a subset of 20 consensus-significant host-associated k-mers, which are significantly overrepresented in a specific host. Surprisingly for host prediction, both the final model with the top 5 k-mers and the simplest model with only the most important k-mer achieved a high classification accuracy of 98%, giving a simple target for predicting host species and cross-species transmission of S. aureus. The final classifier with the top 5 k-mers revealed that 97.5% of S. aureus isolates from livestock-exposed workers were predicted as pig origin, suggesting a high cross-species transmission risk. The time-based phylogeny inferred the cross-species transmission directions, indicating that ST9 can cross-species spread from animals to humans while ST59 can cross-species spread in the opposite direction.

Conclusion: Our findings provide novel insights into host-associated determinants and an accurate model for inferring S. aureus host species and cross-species transmission.

Background: Orobanche is a parasitic plant distributed in the temperate zone of Northern Hemisphere, with approximately 200 species found worldwide. In the Republic of Korea, two species of Orobanche, namely O. coerulescens Stephan ex Willd. and O. filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin, are present, with O. filicicola being endemic. Genome analysis of this species has not yet been performed, and characterizing its complete organelle genome will provide valuable insights into the phylogeny and genome evolution of parasitic plants.

Results: The chloroplast and mitochondrial genomes were analyzed, revealing distinct characteristics. The chloroplast genome is 91,529 bp long with a GC content of 33.6%, containing 33 protein-coding, 30 tRNA, and 4 rRNA genes. In contrast, the mitochondrial genome is 1,058,991 bp long with a GC content of 45.5%, featuring 31 protein-coding, 16 tRNA, and 3 rRNA genes. The mitochondrial genome has over three times more simple sequence repeats and longer long repeats than the chloroplast genome. Analysis of synonymous codon usage in protein-coding genes from nine Orobanchaceae species revealed significant differences between chloroplasts and mitochondria, with codons ending in A or T exhibiting higher coding rates. Ka/Ks ratio calculations indicated that psbI and atpB had the smallest and largest ratios in chloroplasts, respectively, while ccmFC was identified as the only gene under positive selection in mitochondria genomes. Sequence alignment identified 30 homologous fragments between the two genomes, totaling 7,247 bp. Comparison of O. filicicola's chloroplast genome with related species showed gene loss and conserved inverted repeat sequences. Numerous homologous collinear blocks were found in mitochondrial genomes of related species, but some regions lacked homology. Phylogenetic analysis indicated identical topologies for chloroplasts and mitochondria, with Orobanchaceae forming a strong monophyletic group.

Conclusions: Characterizing the complete organelle genome of O. filicicola enabled a comprehensive analysis of the Orobanchaceae organelle genome, providing important baseline data for its structure and evolution.

Background: Temperature is one of the essential abiotic factors required for honey bee survival and pollination. Apart from its role as a major contributor to colony collapse disorder (CCD), it also affects honey bee physiology and behavior. Temperature-stress induces differential expression of genes related to protein synthesis and metabolic regulation, correlating with impaired gland function. This phenomenon has been confirmed in mandibular glands (MGs), but not in Hypopharyngeal glands (HGs), potentially affecting larval nutrition. RNA-seq analysis was performed using HGs tissue at low (23 °C), regular (26 °C), and high (29 °C) ambient temperatures. This study aims to decode molecular signatures and the pathways of the HGs tissue in response to temperature-stress and the rapid genetic changes that impact not only royal jelly (RJ) production potential but also other biological functions related to HGs and beyond.

Results: From the analyzed RNA-seq data, 1,465 significantly differentially expressed genes (DEGs) were identified across all the temperature groups. Eight genes (APD-1, LOC100577569, LOC100577883, LOC113218757, LOC408769, LOC409318, LOC412162, OBP18) were commonly expressed in all groups, while 415 (28.3%) of the total genes were exclusively expressed under temperature-stress. The DEGs were categorized into 14 functional groups and significantly enriched in response to external stimuli, response to abiotic stimuli, and protein processing in the endoplasmic reticulum (ER). Pathway analysis of exclusively temperature-stressed DEGs revealed that these genes promote ECM-receptor interaction and fatty acid metabolism while reducing protein processing in the ER, which is related to royal jelly (RJ) production and overall nutrition. Although heat-shock protein 90 and gustatory receptor 10 serve as markers for stress and hypopharyngeal glands (HGs) development respectively, their expression varies under temperature-stress conditions.

Conclusions: We conclude that with the recent effects of climate change and its contributing factors, honey bee pollination, and reproduction activity is on the verge of halting or experiencing a detrimental decline. Considering the impact of temperature-stress on the expression of the nutritional marker gene (GR10), silencing GR10 in HGs tissue could provide valuable insights into its significance in nutritional performance, survival, and beyond. Finally, a broader temperature range in future experiments could help derive more definitive conclusion.

Background: Primary cardiomyopathies are major causes of heart failure, placing a substantial burden on both individuals and society. Revealing its genetic profiles can lead to a better understanding of the mechanism and is critical for disease prevention and treatment.

Method: Primary cardiomyopathy patients were enrolled and whole exome sequence was conducted to analyze their genetic profiles. Retrospective clinical information extraction and analysis of sequence data were implemented.

Results: A total of 77 primary cardiomyopathy patients were enrolled, comprising 65 patients with dilated cardiomyopathy (DCM) and 12 with hypertrophic cardiomyopathy (HCM). Among the DCM patients, 13 variants classified as pathogenic (P) or likely pathogenic (LP) were identified in 12 patients (18.46%), predominantly in genes associated with the nuclear envelope and sarcomere. Among HCM patients, 6 P/LP variants were discovered in 6 (50%) patients. Taking variants of uncertain significance (VUS) into consideration, an analysis of the association between the number of variants carried by patients and their clinical characteristics revealed that DCM patients with more than one variant had a higher proportion of hyperuricemia.

Conclusions: We map a comprehensive profile of primary cardiomyopathy in Chinese population and, for the first time, identify a possible association between hyperuricemia and the number of genetic variants carried by DCM patients.

Background: Inbreeding, a central theme in evolutionary and conservation biology, is a crucial practice in breeding to stabilize and enhance the specific traits or to establish inbred lines. It also carries the risk of inbreeding depression, reduced fitness, and increased potential for extinction. Nevertheless, inbreeding has been extensively studied in small and endangered populations but its effects in large domesticated animals are poorly understood. Here, we aim to investigate the genomic consequences of inbreeding in the Banna miniature inbred pig (BN), a breed that has been inbred for over 40 years.

Results: We have sequenced 41 genomes of BN and Diannan miniature pig (DN) at high-coverage (> 31×) and combined them with published whole-genomes of swine to comprehensively investigate the genetic consequences of inbreeding. We find that BN is genetically closely related to DN, which is consistent with breeding records. All families of BN have undergone an extreme bottleneck due to intensive inbreeding, resulting in higher genomic inbreeding coefficients, reduced genetic diversity, and a lower effective population size (Ne) compare to non-inbred pigs. Furthermore, BN and DN exhibit an increased genetic load relative to Asian wild boars. Prolonged inbreeding and bottlenecks have led to some purging of deleterious mutations in BN compared to DN, and a conversion from masked load to realized load.

Conclusions: We present a comprehensive analysis to understand and assess the consequences of inbreeding in miniature inbred pigs from a perspective of population genomics. Utilizing genomic measurements proves effective in estimating the consequences of inbreeding, especially when a detailed and accurate historical record of pedigree are lacking. Our results provide valuable resources and a detailed perspective on the genomic impacts of inbreeding, potentially guiding efforts in breeding, breed improvement, and conservation.

Reactive oxygen species (ROS) serve as signal molecules in plant defense responses, and the respiratory burst oxidase homolog (RBOH) enzyme plays a crucial role in their production. Although numerous RBOH family members have been identified in various plants, little is known about the RBOH genes in blueberries. In this study, we identified six VcRBOH genes from the blueberry genome. Phylogenetic analysis revealed that these VcRBOH genes can be classified into three subgroups. Conserved domain and motif analysis demonstrated high sequence similarity among VcRBOH proteins. Analysis of cis-acting elements suggested that VcRBOH genes may be involved in stress, light, and phytohormone responsiveness. Based on transcriptome data, we observed low expression levels of VcRBOHB, VcRBOHC, and VcRBOHE during the flower_at_anthesis stage. In contrast, VcRBOHA and VcRBOHD showed relatively high expression levels in various tissues. The reverse-transcription quantitative PCR (RT-qPCR) analysis indicated rapid induction of VcRBOHF by flg22 and chitin treatments. Notably, overexpression of VcRBOHF in Arabidopsis promoted PTI responses, including increased expression of marker genes, ROS production, and callose deposition. Moreover, the overexpression of VcRBOHF resulted in enhanced disease resistance against Pseudomonas syringae pv. tomato (Pst) DC3000 infection. These findings provide valuable insights into the roles of VcRBOHF genes in plant defense responses and lay the groundwork for a more comprehensive understanding of the molecular mechanisms underpinning blueberry disease resistance.

Background: The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

Main text: Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

Conclusion: This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Background: Poplars are important woody plants, which are widely distributed in the forests from the subtropics to the north of the Northern Hemisphere. Poplars have high ecological and economic value. However, there are frequent interspecific and intraspecific hybrids in Populus, resulting in a large number of intermediate taxa, which makes the morphological identification of Populus very challenging. Plastid genome is an important tool to study the evolutionary relationship of plants. Therefore, comparison and phylogenetic analysis were carried out based on the population chloroplast genomes of 34 individuals from 7 taxa.

Results: In this study, seven newly assembled and annotated chloroplast genomes of Populus were reported. They all had typical quadripartite structures with the same GC content (37.6%), but there were differences within the population, and the genome size ranged from 155,736 bp to 156,812 bp. In all Populus species, 134 genes were identified, including 88 protein coding genes (PCGs), 37 tRNA and 8 rRNA genes. The gene sequences alignment of different taxa showed that the gene sequences and content were relatively conservative, there was no gene rearrangement, and only 3 highly variable regions (psbZ-trnG, ndhC-trnV and trnN-trnR) were identified, which can be used as molecular markers. Most PCGs had high codon usage bias and 3 positive selection genes (rps7, rps12 and rpl16) have been identified. The analysis of population genetic structure and phylogeny showed that the chloroplast genomes supported that Populus was a monophyletic taxon, which could be divided into four sections (Abaso, Turanga, Populus and ATL (Aigeiros, Tacamahaca and Leucoides)). Among them, P. dafengensis, P. butuoensis and P. szechuanica had the closest genetic relationship, P. gonggaensis and P. cathayana had the closest genetic relationship, it was speculated that the taxa of Sect. Tacamahaca may be the main female parent of the three new taxa from Sect. Leucoides.

Conclusion: In general, this study provides valuable insights for new species identification, phylogenetic relationships, breeding and resource development, and genetic diversity of Populus.

Progesterone (P4) is an endogenous sex steroid hormone involved in the ovulatory cycle and pregnancy of animal species. In sheep and goats, P4 analogues are used to induce synchronized ovulations and oestrus behavior of the females. In humans, P4 from chemical synthesis is used to treat peri-menopausal disorders. However, such molecules are released into aquatic environment and can be a source of pollution, are prohibited in organic farms and go against the trend of "naturality" in animal production as well as in human health. A natural alternative may consist in the extraction and use of P4 in plants. Mammalian hormones were discovered in an increasing number of plant species, including walnut leaves that contain high levels of P4. We compared the content of P4 in leaves of 170 accessions of Juglans regia from the walnut germplasm collection of INRAE Prunus-Juglans Biological Resources Center previously genotyped using the Axiom™ J. regia 700 K SNP array. We conducted a genome-wide association study (GWAS) using multi-locus models. When collected in October, P4 content goes from 34,1 to 287,5 mg/kg dry weight of leaves. The two laciniate accessions have the largest P4 content. We identified seven significant marker-trait associations on chromosomes 1, 2, 3, 6, 7, 15 and 16, and a candidate gene involved in the metabolism of sterols, precursors of plant steroid hormones. Our results raise the huge variability of P4 content within J. regia and propose a candidate gene which may have a role in the control of this variability, opening the way to a potential use of walnut P4 by the pharmaceutical industry towards more natural source of chemical compounds.